Sometimes when looping a section of a project that has duplicated tracks, eg a DI bass part blended with an amped bass part, I will hear them go out of phase. Quite significantly, to the extent that the tone changes a lot. Most of the time it can be fixed by stopping playback and starting again. It doesn't occur during normal non-looping playback, but obviously it can be an issue when you're looping a section during mixdown.

Could this be part of the same problem that makes MIDI timing go off slightly when looping? I have the metronome playing on silent as per the workaround, but this doesn't fix the phase issue. Has anyone else experienced anything like this?

I'm thinking maybe an issue with Plug-in Delay Compensation. Are you running any plugs that require it?
 
It would also be worth checking to see whether the issue with non-zero input gain causing MIDI-Audio sync errors on looping could affect sync between two audio tracks.
 
 
 

Don't a lot of plugs report latency for PDC? Anyway, if it's that, it's definitely something that needs to be addressed when looping. It's definitely not the non-zero gain problem, I haven't touched the gain on those tracks.