Thank you for your reply, it is appreciated!
Yes, as you suggested I will in all likelihood be forced to submit a separate paper form 5329 and check to the IRS. Not the end of the world, but it reflects poorly on Intuit when TurboTax offers a feature that is broken, and there doesn't seem to be any simple way to report it to them to fix it so that I can combine the 5329 with my 1040 and e-file both.
