I've seen tracks improperly compensated before, where the result is wrong if I rely on ADC but correct when manually moving the clips the reported amount. I haven't seen things fall out of sync like the OP but to be honest, it could very easily happen and I'd never notice a frame or two on something like an ambience track.
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Maybe related, maybe not, but I sometimes have it, that tracks with plugins suddenly stop being played back.
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I have had this happen before, as recently as a couple of weeks ago. A random track goes mute (no meter moves) for no reason. Relaunch PT.