Bounce track in place moving audio

After some processing I bounce tracks in place to preserve CPU, but when the new .bip track is created the audio has been moved so that it's no longer aligned with the rest of the track. Seems like the offset is always somewhere around 140-160 ticks. It's been happening quite often and is making my mixing take way longer because every time I bounce a track in place I have to manually move things around, and sometimes the groove gets compromised. Has anyone else encountered this? Any workarounds?

I'm working with OS X Yosemite 10.10.5, Logic Pro X 10.2 (this was already happening before the update)

Thanks.