A relative of mine who I accompanied to the financial institution encountered a nearly identical situation where the front-office person marked the "Distribution" box instead of the "Transfer" box on the form despite us repeated telling the person "transfer, not rollover" every time the person said "rollover," and we didn't catch it on their unnecessarily complex multi-page form. However, the check was made out to the new account properly so it indeed constituted a transfer. An original Form 1099-R reporting a distribution got issued, but after pressing them to make the correction the back-office people issued a corrected Form 1099-R showing zero for the amount distributed, so nothing of it got reported on my relative's tax return and was never questioned by the IRS. (We discovered later that the particular bank that was the culprit seems to have a history of messing up IRA transactions.)
Hopefully your situation ends up being a little simpler since you caught it earlier than we did.
