I reloaded firmware 20100516 and had the same problem with midi signals being maxed out. Must be a problem with this firmware and something specific to the Synthex v3.1 56i board (I guess). This is a pity because my rotary encoders are the 2-tick per click type and I wanted the Alt-encoders option.
I guess my next step is to get one of these encrypted chips and try the latest firmware to see if the issue is resolved? For now I have reloaded 20091217 and am getting variable levels so can continue my build
At least I have narrowed down the problem.