If you have an FRN on your license (and we're long past the days when licenses didn't have them), there's no reason to get a new FRN.
Here's a possible explanation, learned from attending many VE sessions: every license has two ten-digit numbers: an FRN and a file number. If the FRN on your license wasn't accepted by the FCC, check to make sure you didn't enter the file number by mistake. You wouldn't be the first, or the hundredth, person to do so.
If that's not the problem, then I agree with Glenn: call the ARRL.