problem

I just got the 3.06 version of the JJ OS and i love everything about it. But I just started to experience problems. Now i don't know whether or not this is related to the OS change. I have a sequence recorded with about five tracks in it and i try to record a new track and the audio cuts out and now sound comes out the headphone jack or the stereo out. But sound comes out when I hit hte play button but none of the pads work. And when you look at the program screen all the samples are not assigned anymore. Also the sounds are there and then I change screens and they are gone. Also whenever I go in a new unused track the sounds don't trigger, but in the step edit screen the triggers are there. I am completely mystified.
HELP!!

Did you perform the standard default system reset after loading the new OS?

I keep telling people they've gotta do this to be sure but they don't believe me. POWER ON whilst holding ERASE key.