My wife and I had to have our FPs taken a total of 7 times (me 3, wife 4) before green card approval.
When we first had our FPs taken everything was fine and both our FPs could be read by the electronic scanner. That was in 2001.
Nearly three years later we were called for 2nd FPs. Mine were fine again, but my wife's couldn't be read clearly. She was advised she would probably be recalled to do them again, and she was. Guess what, the same thing happened when she tried next time (why should it be any different?), and the next.
Finally after letters from our company lawyer, and my wife speaking with the officer at the FP center on her final failed trip, we received notices to attend an "interview" at San Francisco. In lieu of the criminal background checks that would normally take place with your FPs, my wife effectively had to "self-certify" by getting written declarations from each of the three counties' Sherrif's Dept. to say that they had no record of her behaving criminally. That worked fine for 2 out of three of the counties, and the third said "no we don't do those any more". So we got a letter from that county stating their position, and hoped that the immigration offficer would understand that we had done everything we could.
In the end (after another approx 5-6 months of waiting) we were requested to take a mountain of paperwork to the SF BCIS office for the interview. We were treated very courteously, asked a few questions, but really everything was straightforward.
We would recommend you do everything you can to maintain legible fingerprints. We didn't realize they could "wear out".
It's painful just to re-visit that FP process. We're quite sure it would have continued on and on had we not requested a lawyer's letter.