your fader doesn't pass audio when the computer is up and running? this is of course not normal.
the console will act weird if you fire up buckets after the computer booted up already. nothing as dramatic as no audio, but some channels probably won't cut from the group cuts etc. rebooting (type 'BEGIN') usually fixes all of that.
sound wise, 'MO ON' has no vca in the circuit (but the extra audio path in the fader itself), and sounds a bit cleaner / better, at least that's what most people claim. i also find it a bit more 'direct' sounding, but those later revision vcas sound VERY transparent too.
the other reason you might hear a slight difference when you toggle between both modes is the fader alignment.
i do this at least quarter yearly, and some of them drift quite a bit.
the other weird thing is that some faders seem to be super stable throughout the whole path (not necessarily only newer ones), while others have 'problem areas', where you're lucky to get them +-1dB between vca and motor.
i think the reality is that ultimation is great when it works, but other systems, like flying faders, are a lot more sophisticated and stable.
there's also only a small handful of techs that know how to repair faulty modules.
i heard about the 'no computer' solution not really working from various ssl techs as well, peter might've even been one of them, but not sure.
if there's anybody out there who's comfortable fixing fader cards, i have around 20 faulty ones, and would be up for a 'fix one, keep one for free' deal.