I like that it's got its own box now instead of just being lumped in with federal withholding.

I would be surprised if the software does not do this correctly.  The tax withheld on the W-2 and the tax calculated on the 8959 are not always the same.  They may be different depending on filing status and/or other income on the return.  The math is easy enough though.  If you think the software is wrong just walk through the tax calculations on the form.  Then manually subtract the 0.0145% "regular" Medicare tax from the total Medicare withholding on the W-2s to arrive at Additional Medicare withholding.

Edit: Doh!  Got a text I had to reply to and Denise jumped in front of me while I was writing this! 🙂