I had a similar thing. It was a factory preset that had a wah block in bypass mode. When I turned on the Axe & it started up on this preset, the wah was on. I have not done anything with any wah blocks on any preset as I have not yet hooked any pedals, midi or otherwise, to the Axe. I tried to manually bypass it from the front panel, non responsive. Tried to delete it, nothing. Tried to edit it, would not respond to any changes. The only way to clear it was to switch to another preset & back, then the wah was back to being bypassed as it was supposed to be & became editable. It only happened once so I didn't think much of it but it sounds like a similar problem. The preset's wah block becomes engaged & unresponsive to any changes.