You have to save the changes to corresponding Stompbox slot which is used by multiple patches in order to have them in all these patches. So by saving just the preset you don't save the Stompbox settings and new values become PATCH type referring to that patch only.I have to admit I find the Stompbox mode and the way it is described in the manual rather confusing myself.
My understanding is that when you have saved something to stompbox you can use that setting in other presets as well. As a sort of global block. But if you make changes to it in one preset it automatically changes those settings in other presets as well. Is that correct?