Let's start over, one step at a time.
When you got the check from work they probably took withholding out of it, right? The Retirement 1099R should be on 1040 line 16. The full amount of the distribution should be on line 16a. Then line 16b will say ROLLOVER by it and the taxable amount should only be for the withholding amount from 1099R box 4 (since you didn't put the withholding into the IRA). The withholding also shows up on line 64 with any other withholding.
Then the IRA distribution will be on 1040 line 15. The full amount should be taxable on line 15b. So line 15b and 16b should equal the full gross amount of the retirement distribution (before withholding). Then the whole amount is only taxed once.
You said you only reported the 1099R from the bank IRA. You still need to add the retirement 1099R to line 16. It should only add the withholding amount as taxable to line 16b. Does the IRS say you can amend? But you will also get credit for the withholding in box 1099R.
