Tried to reset, change the wires in places on the miner, Yang JYan from the support of the pangolin, installed a new program, nothing helped. They say it's good. I see that this is not normal at all. Probably, this SM2 board does not gain strength, and because of this, everything is overloaded. What do you think controller?
I suggested controller, because of the red diode flashing, and the information you found about the controller checking for errors. I could be totally wrong, but it seems like it keeps checking after upfreq1 is near stable, going to upfreq2. 635/636 is the normal range on mine.
When it hits 635, my miner increases fan rpm, and the hashrate quickly rises. Sometimes at this point the "up time" in the top left corner of cgminer restarts, as if there was a reboot. Sounds like this is the point where your issue is.
When you start the miner, and cgminer loads, how many "active chips" are displayed? If it's a different number on one of the Boards, then that's probably the sign.
Have you tried a different power supply? Pangolinminer has had issues with them recently.