What happened with you sounds to me as a timecode break. I read that, even when there are no timecode breaks on the tape, the camera could cause timecode breaks when the heads need to be cleaned.
Maybe worth a try?
What you describe about clips sometimes not appearing in the bin, but only in the capture scratch, I’ve seen that too. that’s not my problem today. I don’t know yet why it happened, but on another computer the problem didn’t occur… if I find out what caused it, I’ll post it here.