My problem is far simpler and I'm not using Mixpad or any other software. Just crescendo. it happens every time, even with one measure: C chord quarter note, (Middle C, E, G, High C) then a quarter rest, then the same C chord. I play it back and the second chord has only the middle C play just slightly ahead of the other 3 notes of the chord. The same thing happens if I'm using a drum kit. I'm using a MacBook Pro.
If I play just the second chord, it's fine. If play the C chord as a half-note, followed immediately by the same C chord as a half note, I get the same problem. I'm sure that if everyone had this problem, you would obviously not have any users or your user board would be packed with complaints, so I'm guessing that it's my system. Possible memory issue?