Now that you’ve clarified you’re sending a PC message along with a CC# there is a known issue we are looking to resolve regarding these simultaneous messages. I’m certain it’s a the root of the issue. One option is to recall the program in an already bypassed state if it must start off bypassed.
https://www.eventideaudio.com/forums/topic/eventide-h90-midi-pc-change-and-bypass-at-the-same-time/
