Playback not always synced between instruments.
Certain instruments will sometimes play out of sync with others. I have yet to notice a consistent pattern as to what types of material cause this to happen, but it appears to happen consistently when playing back certain sections. It seems to always be that an instrument is lagging a bit behind the beat. This problem still occurs when soloing the responsible parts (using the metronome as the reference guide).
I have also noticed this sometimes occurring simultaneously with some slightly out-of-tune tracks (parts playing back a note a few cents too sharp), though this is perhaps a separate issue.
I suppose the workaround here is to just use a VST or the basic soundfont.