did you resolve your problem? I'd be interested how you did it.
My Variax 300 is faulting in the same way as you describe yours. The problem seems to occur when using custom altered tunings and has only started occuring in the last couple of months. All of my Custom 1 bank are alternate tunings I've created myself but havent had any trouble with them in the past.
I'll try cleaning the connections as suggested in another thread about a similar random patch change problem. Have just got a new computer and not put workbench or monkey on it yet so if a clean does not work will hook up work bench and try what Line6Hugo recommended in the post above.
Incidentally, this guitar developed a random patch changing problem about 18 months after I got it and the dealers here repaired it under warranty (replaced a circuit board if I recall correctly), but that was about 4 years ago and has been ok until recently.