This could be a bug with Android builds (FMOD Studio Unity 1.09.03 & Unity 5.5.2f1). No problems with stand-alone & iOS builds.
I have single events using up to 8 audio tracks and I use Studio::setMute to mute/unmute the audio tracks individually. For longer loops inside the event (>10 seconds) when muting those tracks quickly in succession they get out of sync in Android builds (tested on multiple devices from 2014 to 2017).
Problem solved with Studio::setVolume, set to a very low value. This doesn’t cause any drift.
Of course it’s possible that I missed something from the docs …