I think it is likely that it started the run by overwriting the same file and then after midnight the sequence started incrementing correctly.

Some additional clues that might help track this down.

I am unable to duplicate it with the simulators.
I have not seen it happen with darks or flats and they never start a sequence with 000 only 001.
I cannot be certain that it has anything to do with the 000 numbering, but it started at the same time, back early last year.
It happens with and without using the scheduler.
It seems to correct itself when midnight occurs.
If it is happening and you stop and start the capture sequence it seems to fix it for the current run.

Paul

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