I know of no circumstances where TurboTax will actually change the amount shown in box 2a on it's own for a code 4G Form 1099-R. However, in the follow-up make sure that you indicate that you did not roll the money over to a Roth 401(k) or Roth 403(b) but that you *did* roll the money over to a Roth IRA. Until you indicate that the money was rolled over to a Roth IRA, it seems that TurboTax will ignore the amount in box 2a (but not zero it).
Also make sure that you have not inadvertently marked the IRA/SEP/SIMPLE box on TurboTax's 1099-R form.
If these don't result in the box 2a amount being reported as the taxable amount, try deleting and reentering the Form 1099-R.
