We've successfully added a number of Custom Fields using the Metadata API.  Our site is an Asp.net and we're using VB for coding (thought about posting to .NET Development, but our question is more API focused).  First we build a Custom Field: 

metaCustomField = New sfMetadata.CustomField
metaCustomField.fullName = "Account.TestField__c"
metaCustomField.description = "Test Field for Account"
metaCustomField.inlineHelpText = "Test Field for Account"
metaCustomField.label = "Field Label"
metaCustomField.length = 20
metaCustomField.lengthSpecified = True
metaCustomField.unique = False

Then we add the Custom Field to an Array of Custom Fields (metaCustomFields).  There are roughly 40 fields, so we limit the array to 10 and submit each batch of 10 fields using:

metaCustomFieldsResult = myMetaService.create(metaCustomFields)

This all works well, and the fields are created as desired.  The first time we created the fields, it worked perfectly and we were then able to use the Soap API to populate the Account object with data (including the custom fields).

However, for some reason, if we delete a Custom Field and then add it again, or if we test using other Salesforce logins, the fields are getting generated properly, but the permissions on the fields are no longer being set (none of the "Field-Level Security" is set to visible).  We're not sure what we changed, but we've begun looking into how to apply Permission Sets to the Custom Fields for the Account object.  There appears to be a couple concepts to consider.  First, we've seen some code for building a package.xml file listing our field permissions and then submitting the zipfile:

<fieldPermissions>
     <editable>true</editable>
     <readable>true</readable>
     <field>Account.TestField__c</field>
</fieldPermissions>

In addition, we noticed that there are some additional Metadata API functions that look like they might help, but we can't find any details or code samples on how to apply them:

' Will adding either of these lines to the
' Custom field definition help:
metaCustomField.visibleLines = 1
metaCustomField.writeRequiresMasterRead = True

' Or, define a Permission Set
metaFieldPermission = New sfMetadata.PermissionSet
' Not sure what to do with it from here...

Can anyone tell us if we are heading in the right direction, or if there is a preferred method for setting the "Visible" Field-Level Security permissions for the custom fields we have created?

We've successfully added a number of Custom Fields using the Metadata API.  Our site is an Asp.net and we're using VB for coding (thought about posting to .NET Development, but our question is more API focused).  First we build a Custom Field: 

metaCustomField = New sfMetadata.CustomField
metaCustomField.fullName = "Account.TestField__c"
metaCustomField.description = "Test Field for Account"
metaCustomField.inlineHelpText = "Test Field for Account"
metaCustomField.label = "Field Label"
metaCustomField.length = 20
metaCustomField.lengthSpecified = True
metaCustomField.unique = False

Then we add the Custom Field to an Array of Custom Fields (metaCustomFields).  There are roughly 40 fields, so we limit the array to 10 and submit each batch of 10 fields using:

metaCustomFieldsResult = myMetaService.create(metaCustomFields)

This all works well, and the fields are created as desired.  The first time we created the fields, it worked perfectly and we were then able to use the Soap API to populate the Account object with data (including the custom fields).

However, for some reason, if we delete a Custom Field and then add it again, or if we test using other Salesforce logins, the fields are getting generated properly, but the permissions on the fields are no longer being set (none of the "Field-Level Security" is set to visible).  We're not sure what we changed, but we've begun looking into how to apply Permission Sets to the Custom Fields for the Account object.  There appears to be a couple concepts to consider.  First, we've seen some code for building a package.xml file listing our field permissions and then submitting the zipfile:

<fieldPermissions>
     <editable>true</editable>
     <readable>true</readable>
     <field>Account.TestField__c</field>
</fieldPermissions>

In addition, we noticed that there are some additional Metadata API functions that look like they might help, but we can't find any details or code samples on how to apply them:

' Will adding either of these lines to the
' Custom field definition help:
metaCustomField.visibleLines = 1
metaCustomField.writeRequiresMasterRead = True

' Or, define a Permission Set
metaFieldPermission = New sfMetadata.PermissionSet
' Not sure what to do with it from here...

Can anyone tell us if we are heading in the right direction, or if there is a preferred method for setting the "Visible" Field-Level Security permissions for the custom fields we have created?