I had the same problem, where my ATRIX would not charge past 90%. Based upon reading the android hackers posts for solutions to this problem I found one that worked for me.
1) Let your battery fall to 0%. (Play a game or something till it shuts itself down)
2) Pull out battery
3) wait 30 seconds put it back in
4) Charge phone from wall mount.DO NOT TURN PHONE ON
5) DO NOT TURN PHONE BACK ON , let it charge while off. Don't press button to check status or anything, just give it enough time fully charge. 5 hours should work.
6) After 5+ hours haveshould elapsed, leaving phone still plugged in, pull out battery
7) After Motorola logo pops up, unplug phone.
8) Put battery back in.
9) Turn on phone. It should now say 100%
Seems there is a battery statistic file that your trying to fix. I read about rooting your phone and running battery calibration tools but my phone isn't rooted and I built this solution trying to reproduce the phone receiving a fresh new battery. I honestly don't know if all the steps are required, but its what I did and it worked for me. Good luck.