In the CD/download version of TurboTax (but not the online version of TurboTax where the implementation with respect to this situation is deficient) you can indicate, when asked, that a different amount than the amount in box 2a is taxable. The CD/download version of TurboTax will then allow you to select the General Rule (which is the correct selection for a nonqualified annuity established in 2000) and then enter the actual taxable amount of around $25k in this case. The CD/download version of TurboTax then just stuffs the actual taxable amount into box 2a of TurboTax's 1099-R form with no other modifications to the form.
The recommendation that you got replicates this behavior, but that there is no need to unmark box 2b Taxable amount not determined. I would leave that marked as long as you see the correct taxable amount included on Form 1040 line 5b.
