Not sure if this is your issue but worth checking. If I forget to disable input quantize when recording a piano track, the resulting playback will horribly accentuate the deficiencies of my timing . With IQ set to something like 1/32, the timing issues sound like little weird glitches. IF IQ is set to 1/4, the source of the prob is obvious. Turning off IQ fixes it in a hurry but of course the parts have to be rerecorded. I don't think IQ can be undone. I know now to always check for it, but the first few times I didnt realize what the cause was and trashed a few projects.
Good luck!