With regards to the sustain pedal, I myself had the very same problem. There is currently (OS3) no option to change this in the software. What I had to do was to reverse the lines in the actual pedal but if you do have a polarity switch on your pedal this really shouldn’t be a problem - and should work.
Maybe buying a Ketron branded sustain pedal would be the best solution.
[This message has been edited by Morten Jonassen (edited 04-02-2010).]