In TurboTax simply indicate that the entire distribution was rolled over. The rep is correct that you should include statement explaining why the rollover contribution amount on the Form 5498 does not agree with the amount claimed as rolled over. TurboTax does not have a provision for doing this by e-filing, so you'll need to print and mail your tax return to include your separately prepared statement.
Be sure to tell TurboTax that none of the distribution was RMD. If you already told TurboTax that some amount of this distribution was RMD, delete and reenter the Form 1099-R.
