I just downloaded episode 100 of Prince of Tennis, and noticed that after AOM renamed, it wa out of order, because all of the other episodes were numbered with two digits...
i.e.
Prince of Tennis 09
Prince of Tennis 10
Prince of Tennis 100
Prince of Tennis 11
The other long series I have are fine. My guess is that AOM determines the number of digits based on the number of episodes (99), not the largest episode number (101). Since PoT had a couple of specials that counted as 2 episodes, they skipped a couple of episode numbers. If this is the case, it will forrect itself in a couple of episodes, but atm it is wrong.
BTW, I believe that this is an AOM bug and not a AniDB bug because for One piece, AOM uses 3 digits and AniDB uses 2 digits for the ed2k links.