I'll check it out later. It's Ironhead's AI, right?
I think CLR and CLO do the same thing, but CLO also closes the message box (which CLR doesn't do). I also shortened all text to "text" (
) to get to the action faster while investigating.
Skip flags 0001 to 0063 are saved on a soft reset, as far as I've been told.
I don't know if SK+5000 is also saved (or if it's just a normal flag being set this way) though.