If all amounts distributed from IRAs were rolled over, the amount on line 15b should be zero. Line 15b should not be the total of the amounts in box 2a of the Forms 1099-R since a Form 1099-R reporting a regular distribution from a traditional IRA must always have box 2a equal to the amount in box 1 and have box 2b Taxable amount not determined to be marked whether or not the distribution is taxable. It's impossible for an IRA custodian to determine the actual taxable amount of any regular traditional IRA distribution.
You said that the problem is that the IRS does not agree that the ROLLOVER notation is present for line 15 despite it being present on your printed copy. Check your tax return transcript for the year downloaded from the IRS to confirm that this is the case. Check your Wage & Income transcript for the the to see that it includes Form 5498 from this IRA showing the rollover contribution in box 2. I don't see how it's possible for your e-filed Form 1040 could have line 15b be zero (correct) but not have the ROLLOVER notation (incorrect), so it seems more likely that the IRS is missing the Form 5498 corroborating the rollover. The only way I can see that your printed copy would be different from what was e-filed is if you changed your entries between the time you filed and the time you printed.
https://www.irs.gov/individuals/get-transcript
