Hmm, I had the same issue once, but then realized that I did a misconfiguration: I had both Wah and Vol set to Exp1 (which resulted in a similar behaviour. As soon as I changed Vol to Exp 2 and had in Default only one of the two switched on everything worked smoothly.
Just to add: I am using FBV3 with a Pod HD Pro X rack unit and Pod HE Edit Software ...