Richard:
I just got this problem wrong, playing the completely winning 1.Re3, and lost 11 rating points. Too bad I didn't remember this forum discussion.
Anyway, there is really an urgent need for manual disabling of problems. It's extremely frustrating to play a forced win and get marked wrong, especially when you lose a lot more for wrong problems than you get for correct problems.
There aren't many of these problems, but it's really needed to just disable them now. No coding is needed, I don't think. You mentioned you don't have the code to keep the problems disabled after a future generator run. Well, pencil and paper can keep a list of problems that should remain disabled, without any coding

Rybka, with NO tablebases, says +4.92 for 1.Re3 after 5 seconds of thinking. I don't know what the problem is with Toga. Tablebases are not needed for an engine to see that 1.Re3 wins. And certainly I hope we don't have to wait for a new generator run with tablebases before the endgame problems with errors get disabled.