I now have the same issue. I have no idea what I did but I could always adjust vol and pan on HS3 from the track inspector and the mix console. As of a few days ago, I have to do it from the Quick controls in track inspector or directly in HS3.
Strangely enough, this does not occur on other vst instruments, just HS3. This is a clue that I should look at the Cubase/Halion communication. I am still searching for an answer. If someone with more experience than I can help, I could stop searching and continue playing.