Yup. Did all there is to do, in various orders. Nothing helped. Only changing the OS.
I've had even more peculiar problems though, so I wasn't too surprised. One particular OS "transposed" all NRPN's up 120 steps. Just that particular OS, so I degraded to the previous OS until an even newer OS was released that worked fine (in this regard). I tried several OS's during my trouble-shooting, re-calibrating etc etc, to try to find an explanation, but nothing. I posted about it here, but it seems noone had experienced the same problem (of those who use NRPN's). Still, noone has a clue as to how or why this could and did happen, afaik.
I don't see a point in trying to find out why things don't work on the Rev2 anymore, ie troubleshooting, as sometimes there seem to be specific bugs to specific units. Or as in this case, reverse bug behaviors between different units and OS's.
It's like the Rev2 is haunted.