I moved all the volume and tone knobs around a bit now. I haven't used them in a while except the master volume knob. I've been doing all my changes through the desktop software for about the last 6 weeks. I can't notice the problem anymore, maybe that was the issue. I didn't notice the problem until I was playing live on sunday, and after re engaging a footswtich, it was hard to hear myself because I was next to the drummer. I know to be careful to not touch the tone/EQ knobs on stage because it will temporarily change the saved settings. It kept on happening throughout the worship service, and up until yesterday it was still happening. It seems to be fine now. I may end up temporarily taping the knobs at 0 next time I'm on stage, and see if the problem reoccurs.
Thanks for your input guys.
And when you say re installing the firmware, do you mean the flash memory through the monkey software?