It's a far shot, BUT, I have seen guitar effect boxes that will oscillate with certain types or brands of 9V battery. The Pro 96 is a digital machine and VASTLY more complex than the box I've seen do this but it is perhaps comparable. I believe this may be related to the different internal resistance of different battery types.
I've used 1800mAh NiMH and 2300 mAH NiMh made by or for Lenmar Battery Solutions.
No problem and they've been great. Never tried a NiCad with it....
What brand and type battery are you having trouble with?
-Jon