I misunderstood your previous comment as indicating that the IRS had finally been satisfied that this was a rollover.
I commented on one other case like this on the TurboTax forums several years ago and in that case the person had similar difficulties in getting the IRS to recognize that this was a rollover. However, in that case I think the loss of the ROLLOVER indication was the result of a date transcription error of a mailed the tax return. In case like that it does seem that you have to treat what the IRS presently says as what you actually filed and amend to correct the IRS's position. In this case it might be appropriate to include a copy of the correct Form 1040 along with Form 1040X so that you can highlight the ROLLOVER notation that appears in the left-hand margin next to line 15. It might not hurt to also include a copy of your Form 5498 showing the rollover contribution to the receiving IRA or an account statement showing deposit into the account of a qualified retirement plan, whichever applies.
Just make sure that the Form 1099-R reporting this distribution actually did have the IRA/SEP/SIMPLE box marked indicating that the distribution was from an IRA and not from a qualified retirement plan like a 401(k) so that it was proper that the distribution and rollover indication is reported on line 15.
