So I don't know why I never really had this issue in Sonar 8.5 (not really never, sometimes I did, but far far less)... But I have it almost every single time in X3.
So I go hit record, I start playing my keyboard, until I have a nice little melody/progression that works. Lets say for the sake of the story its a 4 bar loop and the part I like is from bar 4 to bar 8. I also quantized it at 1/8th notes. So with snap on, I cut it at bar 4, I cut it at bar 8, delete everything before and after, and proceed to drag out some copies to repeat that little piece. Like 90% of the time, it looks perfect, but when I play back I notice a hesitation. So sure enough I go in, and there was the tiniest of tiny little blank space before the first note in the progression, leaving all the copies off by a little bit. The first note doesn't start at 4:01:000 it's at like 4:01:xxx some random little number. Not even a nicely quantized number even though the whole thing was selected when I hit quantize.
So obviously I then delete all the copies I had made, right click the original, hit Apply Trimming, drag the clip that little tiny fraction of a bit back to start at 4:01:000 and then make my copies and all is right. It's just annoying and if there's something I'm not doing that would save me that hassle I'd love to know.
Thanks!