This has been driving me mad over the last few months. I have contacted Line 6 about it and they said that this is the first they've heard of it, so hopefully will get a proper fix soon, I'm sure it will!
The other workaround was when I transferred some hx stomp presets over that already had the wah programmed to change in this fashion, it worked on the stadium when it was transported over. Then I used that preset as a template for the others to have the bypassing working properly