I'm having the same issue w/my POD HD Pro and it's driving me mad! I go direct into the board and I'm really pissing off every sound guy we've worked with (including our own).
I set the channel volume w/the Volume knob to 50%, save x2, switch to next patch, switch back, volume too loud again at 70%. I view knob settings -- volume dot is where I'd set it (50%) but the dial was around 70%.
I originally thought it was on any patch I set to bank 3A. When I saved this patch to another bank, however, the same thing happened.
I will double-check the volume pedal setting and make sure it matches the 50% -- I didn't consider this to be the issue since I don't move the volume pedal at all when I'm setting the volume & switching back-and-forth between patches to check levels.