I updated the SendEmail.cls to allow me to set the Organisation Wide Email address. This now works sweet: 

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* Salesforce version written for: Winter '12 onwards
* This Apex plug-in for Visual Workflow is a wrapper on top of the standard SendEmail API to send emails
* This Apex plug-in also supports the ability to send a PDF attachment.
*
* Inputs:
*  recordID (String)  - Optional
*  orgWideEmailAddressId (String)  - Optional
*  emailAddress (String) - Optional
*  subject (String) - Required
*  body (String) - Required
*  textAttachmentName (String) - Required
*  textAttachmentBody (String) - Required
*  pdfAttachmentName (String) - Required
*  pdfAttachmentBody (String) - Required
*
* Outputs:
*  Status (String) - SUCCESS/ERROR
*  ErrorMessage(String) - 'Email sent successfully'
*/


// The Apex Plug-in for a flow must implement the Apex Process.Plugin Interface
global with sharing class SendOrgWideEmail implements Process.Plugin {

    public String pluginStatus;
    public String pluginErrorMessage;
   
    public static final String SUCCESS = 'SUCCESS';
    public static final String ERROR = 'ERROR';
    public static final String SUCCESS_MESSAGE = 'Email sent successfully';

   
   
    /* The main class called by the engine at run-time
     *
     * Inputs:
     *  recordID - Value set in the setTargetObjectId call to SendSingleEmail
     *  orgWideEmailAddressId (String) - set the "From Address" of the email
     *  emailAddress (String) - set the "To Address" of the email
     *  subject (String) - Self explanatory
     *  body (String) - Self Explanaory
     *  textAttachmentName (String) - Name of the attachment to be sent. The attachment is added to the
     *              attachments section if a record ID is set as long as the record ID is not a User.
     *  textAttachmentBody (String) - Body of the attachment recorded in the attachments related list
     *  pdfAttachmentName (String) - Should contain ".pdf" to convert the pdfAttachmentBody to pdf.
     *  pdfAttachmentBody (String) - PDF body of the attachment.
     *
     * Outputs:
     *  Status (String) - SUCCESS/ERROR
     *  ErrorMessage(String) - 'Email sent successfully'
     */
   
        global Process.PluginResult invoke(Process.PluginRequest request) {   

        // Get all the inputs from the Flow
        String recordID = (String) request.inputParameters.get('recordID');
        String orgWideEmailAddressId = (String) request.inputParameters.get('orgWideEmailAddressId');
        String emailAddress = (String) request.inputParameters.get('emailAddress');
        String subject = (String) request.inputParameters.get('subject');
        String body = (String) request.inputParameters.get('body');
      
        //Get the list of Attachments
        String textAttachmentName = (String) request.inputParameters.get('textAttachmentName');
        String textAttachmentContent = (String) request.inputParameters.get('textAttachmentContent');
        String pdfAttachmentName = (String) request.inputParameters.get('pdfAttachmentName');
        String pdfAttachmentContent = (String) request.inputParameters.get('pdfAttachmentContent');
           
    Map<String,Object> attachments = new Map<String,Object>();
    if ( (textAttachmentName !=null &&  textAttachmentName.length() > 0) && (textAttachmentContent !=null &&  textAttachmentContent.length() > 0))
            attachments.put(textAttachmentName, textAttachmentContent);

     if ( (pdfAttachmentName !=null &&  pdfAttachmentName.length() > 0) && (pdfAttachmentContent !=null &&  pdfAttachmentContent.length() > 0))
           if(!pdfAttachmentName.contains('.pdf')) pdfAttachmentName = pdfAttachmentName+'.pdf';
            attachments.put(pdfAttachmentName, pdfAttachmentContent); 
                    
    Map<String,Object> result = new Map<String,Object>();
    try {
        //Send email
        SendEmail(recordID, orgWideEmailAddressId, emailAddress, subject, attachments,body);
        result.put('Status', pluginStatus);
        result.put('ErrorMessage', pluginErrorMessage);
    }
    catch (Exception anException) {
        result.put('Status',ERROR);
        result.put('ErrorMessage', anException.getMessage());

    }
    
        return new Process.PluginResult(result);
    }
   
    /**
     * Implementation of the SendMail Apex plug-in
     */
    global void sendEmail(
        String recordId,
    String orgWideEmailAddressId,
        String emailAddress,
        String subject,
        Map<String,Object> attachments,
        String body
    ) {
        Messaging.SingleEmailMessage message = new Messaging.SingleEmailMessage();
        Boolean recordIdIsUser = (recordId != null) && recordId.startsWith('005'); //is the record id referencing a user id?
        Boolean saveAsActivity = !recordIdIsUser;
        if (emailAddress != null && emailAddress.length() > 0) {
            message.setToAddresses(new String[] {emailAddress});
        }
        if (recordId != null && recordId.length() > 0) {
            message.setTargetObjectId(recordId);
        }
        message.setSubject(subject);
        message.setHtmlBody(body != null ? body : '');  // If the body is empty, use an empty string
        // Don't set the reply to, because it's auto-calculated.
        message.setUseSignature(false);
        message.setSaveAsActivity(saveAsActivity);
        message.setOrgWideEmailAddressId(orgWideEmailAddressId);
       
        // Convert the attachments, creating the objects to add to the list of attachments if set
        List<Messaging.EmailFileAttachment> emailAttachments = new List<Messaging.EmailFileAttachment>();
        List<Attachment> attachmentList = new List<Attachment>();
        if (attachments != null) {
            for (String attachKey : attachments.keySet()) {
                String attachValue = (String) attachments.get(attachKey);
                if (attachValue == null || attachValue.length() == 0) continue;
               
                Messaging.EmailFileAttachment emailAttach = new Messaging.EmailFileAttachment();
                emailAttach.setFileName(attachKey);
                Blob attachment;
                if (attachKey.endsWith('.pdf')) { // if its a pdf need to convert
                    attachment = Blob.toPdf(attachValue);
                } else {
                    attachment = Blob.valueOf(attachValue);
                }
               
                emailAttach.setBody(attachment);
                emailAttachments.add(emailAttach);
               
                if (recordId != null && recordId.length() != 0 && !recordIdIsUser) {
                    Attachment attach = new Attachment();
                    attach.ParentId = recordId;
                    attach.Name = emailAttach.getFileName();
                    attach.Body = emailAttach.getBody();
                    attachmentList.add(attach);
                }
            }
        }
        message.setFileAttachments(emailAttachments);

            Messaging.SendEmailResult result = Messaging.sendEmail(new Messaging.SingleEmailMessage[] {message})[0];

            // If the record ID is specified, add the email to the parent object as well.
            if (attachmentList.size() > 0) {
                insert attachmentList;
            }
            if (result.isSuccess()) {
                pluginStatus =  SUCCESS;
                pluginErrorMessage = SUCCESS_MESSAGE;
            } else {
                pluginStatus = ERROR;
                pluginErrorMessage = result.getErrors()[0].getMessage();
            }
    }


    /* This is the method the Cloud Flow Designer calls to show the Apex Plug-ins to the flow author
     * The implemnetation of this method drives how author of the flow interacts in the the Cloud Flow Designer
     */      
    global Process.PluginDescribeResult describe() {
   
    Process.PluginDescribeResult result = new Process.PluginDescribeResult();
        //Shows the description visible in the Palette tab of the Cloud Flow Designer.   
        result.description = 'The SendEmail Flow Plug-in send an email according to the Messaging.SendSingle Apex API';
       
        //Setting the 'tag' give the Apex Plug-in as its own section on the Cloud Flow Designer Palette tab.
        // Use this attribute to group related Apex Plug-ins together in the Cloud Flow Designer.       
        result.tag = 'Emails';

        //All the Inputs needed, their data type and the requiredness       
        result.inputParameters = new List<Process.PluginDescribeResult.InputParameter>{
            new Process.PluginDescribeResult.InputParameter('recordID',
                Process.PluginDescribeResult.ParameterType.STRING, false),
            new Process.PluginDescribeResult.InputParameter('orgWideEmailAddressId',
                Process.PluginDescribeResult.ParameterType.STRING, true),   
            new Process.PluginDescribeResult.InputParameter('emailAddress',
                Process.PluginDescribeResult.ParameterType.STRING, true),
            new Process.PluginDescribeResult.InputParameter('subject',
                Process.PluginDescribeResult.ParameterType.STRING, true),           
            new Process.PluginDescribeResult.InputParameter('body',
                Process.PluginDescribeResult.ParameterType.STRING, true),
            new Process.PluginDescribeResult.InputParameter('textAttachmentName',
                Process.PluginDescribeResult.ParameterType.STRING, false),
            new Process.PluginDescribeResult.InputParameter('textAttachmentContent',
                Process.PluginDescribeResult.ParameterType.STRING, false),
            new Process.PluginDescribeResult.InputParameter('pdfAttachmentName',
                Process.PluginDescribeResult.ParameterType.STRING, false),
             new Process.PluginDescribeResult.InputParameter('pdfAttachmentContent',
                Process.PluginDescribeResult.ParameterType.STRING, false)
                                                                                                                
                };

        //All the Outputs and their data type
        result.outputParameters = new List<Process.PluginDescribeResult.OutputParameter>{
            new Process.PluginDescribeResult.OutputParameter('Status',
                Process.PluginDescribeResult.ParameterType.STRING),
            new Process.PluginDescribeResult.OutputParameter('ErrorMessage',
                Process.PluginDescribeResult.ParameterType.STRING)                                     
                };
  
       
        return result;
        }
 
    }