I've experienced this quite a few times. I have my amp and guitars are right next to my recording PC and a GUI is better for just messing around.
There are a few problems I've noticed using the edit program, but the crazy wah and volume problem are just weird.
I had a patch set to have a wah on EXP2 (toe switch) and volume on EXP1, high gain patch with a noise gate at the start of the chain and the wah directly after it. Send to POD, unplug - Wah ON, volume not working and the noise gate turns off with the toe switch now; So the wah will be on and the noise gate will be off. Lots of feedback right away
My only solution was to reset all the footswitch assignments to nothing and save, then set it up again and save on the POD itself and not SEND from the software.
Quite annoying. Plus it would be nice if the GUI actually scaled, some of us run higher resolutions than 800x600.