Reikosaka and ExPew asked me to check this out. It appears that the 'Resnap All Notes' feature has a rounding problem, and aimod doesn't pick these unsnapped notes up.
For example, in Azu - Haryu's Another difficulty, some notes are off by 1ms from their correct timing. For example 01:42:705 (102705|6,102705|5,102706|4) - if you notice in the link, one of these notes is 1ms later than the others. The notes directly after those 01:42:844 (102844|3,102844|0) - are also off by 1 ms.
I'm not sure of more examples because 1ms error is hard to find, especially since AIMod doesn't pick them up, but that's no excuse for leaving this unfixed either.
For example, in Azu - Haryu's Another difficulty, some notes are off by 1ms from their correct timing. For example 01:42:705 (102705|6,102705|5,102706|4) - if you notice in the link, one of these notes is 1ms later than the others. The notes directly after those 01:42:844 (102844|3,102844|0) - are also off by 1 ms.
I'm not sure of more examples because 1ms error is hard to find, especially since AIMod doesn't pick them up, but that's no excuse for leaving this unfixed either.