For a properly reported rollover of the entire amount, line 4a will include the amount from box 1 of the Form 1099-R and line 4b will include none of it. The word ROLLOVER will appear next to the line. If the word ROLLOVER is not present, it's not being reported as a rollover.
If you are using the CD/download version of TurboTax, make sure that you have allowed TurboTax to install the latest update.
If your tax return includes multiple 1099-R forms, it might help to delete them all and reenter all of them.
