[jwasbury]

If you've gone over the maximum Social Security tax (stops somewhere around 106k gross wages = $6,621.60 in social security tax for 2009) because you changed employers over the year, good chance you are entitled to a refund of that overpaid amount.

The fact that the social security refund was calculated, but then disappeared when you went through the e-file process sounds fishy to me. It could have something to do with the W-2 data-entry screens not being completely filled out. When you e-file, you need to input ALL the little details from your W-2s (such as the employer's tax ID numbers). FWIW, If you are filing paper returns, you just attach the W-2s and can get away with a lot less data entry into the software.