Hey everyone. I wish I could explain myself better when it comes to describing my problem but I'll do my best. As far as I can tell at the moment, after I record a take, use auto-punch recording to fix mistakes, listen to it (sounds good so far) and save the file. Almost immediately after, I get these "gaps" about the size of one beat(looks likes a quick swipe comp that I can't edit back) in the track that moves everything thereafter earlier or later in time throwing off the sync with the rest of the song.

Hi Engellos, Welcome to the forums :) This sounds like the Take Folder / Quick swipe Bug I've heard of before! Unfortunately, there is no known fix for this yet that I am aware of except to flatten the take folder before saving! Hopefully it'll get addressed in a future update. Cheers Rounik