It was a rewards calculation problem, caused by bug in vardiff handling by the new software. It was impossible to detect this problem using low hashrates, that's why offline testing wasn't helpful.
I hope more people come forward and send the funds back. I've been double-paid by an exchange and a mining pool and always sent the extra funds back. Of course there was a temptation to keep it, but that hurts the entire community as evidenced here.
Good luck and I hope the pool recovers.