The problem you describe is exactly the one I am having. I find it happens only if you switch snapshot with the wah being auto-engaged.
I have a Boss FV-500H.
Yes, I tried all three settings for that parameter without luck.
I have no parameter assigned to the snapshot for that wah, so I guess it should behave exactly the same way in all snapshots.
I should also mention that all snapshots behave as expected if I let the auto-engage enough time to disable the wah before switching preset. It's switching while the wah is auto-engaged that messes everything.
@codamedia 's tip to set snapshot to "discard" works as a workaround, but I have to press the snapshot twice. If I switch to snaphot 1 and get the inverted auto-engaged state, pressing snapshot 1 again fixes the issue. Moving to another preset and back also works as a workaround.