I am glad you figured it out.  The program just looks at the EIN and assumes it is the same employer, in which case you have to get the refund from the employer.  But if it is an agent situation, you have to enter the correct amounts on the 1040 worksheet.  Then I would attach as a PDF your supporting documentation showing that it is an agent situation and also make sure the W-2 input indicates it is an agent situation or IRS is going to bounce it and it will take a really long time to straighten it out, as IRS doesn't understand it themselves.