Setting flags upon clearing memory is certainly repeatable on my CM15A.
This was one of the worse program debugging encounters I have had, with AHP/CM15A. It look me a long, long time to isolate my problem to all my flags being set. I, too, always clear memory before downloading.
I now have a macro which goes thru, and resets all my flags. This way, I have them all in known, intentional, states. I run that macro each time I clear/download a new program.