EDIT: See the orignal post for the solution. Just marking this as solved for other people

EDIT: The notes below are for a hack to fix the missing zero (for double's with a scale of 2 only) and DO NOT read from the meta data to determine if this is the proper setting.  The only time this should cause trouble is if you chose one decmail point in the scale setting.  Please note that it will NOT fix 100.00 to be 100.000 - so if your scale isn't 2 you don't want this hack.  At somepoint, I hope to add code to use the describeSObjectResult function in the API to determine the scale dyanmically and output a value inline with the setting for that field but this isn't that code.

EDIT: this hack only applies to version 19 - update coming soon for version 23

EDIT: for version 23 you need to edit .com.salesforce.dataloader.action.visitor \ PartnerQueryVisitor.java

For anyone interested in updating the data loader such that any fields that currently output ending in .0 being output as .00 instead (i.e. getting 100.00 instead of the current 100.0), here are some notes:

1. Get the code loaded as in the above post.

2. Open QueryVisitor.java (PartnerQueryVistior.Java in v23)

3. Change this line: import java.util.regex.pattern;

To be this line: import java.util.regex.*;

4.  locate the convertFieldValue function.

5. Append this code to the botton of the function (right before the return line):

        if (fieldVal != null) {
            
            // create a pattern to use regular expressions
            Pattern ptrnEndsInDotZero = Pattern.compile("\\.[0-9]");
            Pattern ptrnEndsInDotTwoNums = Pattern.compile("\\.[0-9][0-9]");

            // cast our number to a string
            String strDecimalAmount = fieldVal.toString();
            
            // create a matcher from our pattern and string
            Matcher mtchEndsInDotZero = ptrnEndsInDotZero.matcher(strDecimalAmount);
            Matcher mtchEndsInDotTwoNums = ptrnEndsInDotTwoNums.matcher(strDecimalAmount);
            
            boolean blnDotZeroSearchResult = mtchEndsInDotZero.find(); 
            boolean blnDotTwoNumsSearchResult = mtchEndsInDotTwoNums.find();


            if (blnDotZeroSearchResult == true && blnDotTwoNumsSearchResult == false) {
                // Has tenths but not hundredths
                // found an entry with missing Decimal
                // add the zero back.
                fieldVal = fieldVal + "0";
            }
        }   // check for null field