Manually stretching audio makes track playback faster

[KayN]

I'm trying to sync overdubbed guitar track to an original distorted audio file to perfect the video sync. I'm moving the beats in the sequence editor and everything seems to go right, but when I play long enough, the edited track starts to go ahead of time. If I stop and continue playback from where I was, audio is synced again. Same happens if I merge or bounce the track. The end result is a bit shorter and faster. I can get ok end result if I stretch the merged file a bit longer, but that seems a bit wrong. Anyone have any idea what's going on?