I'd play with adjusting your buffer. The other key to getting arps to sync is to start playback on beat 1 of any bar using your quantise. being slightly out will totally fuck it. that said, they can still drop out and flip out if you repeatedly stop and start sections while mixing/producing, and the only workaround I have found is zen like patience.
that or freezing the arps during intensive microediting/mixing work.
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