Video and MIDI Change Program issue using arrange track

Hello. I´m using my self-designed true 8 bypass (PIC based).
It changes to a pre programmed combination of relays on or off each time it receives a Program Change on its midi in.
It works fine except in those cases i described before.
I´ve the same problem using a Boss GT100 instead… and inclusive with the patches of a sampler or synth in an instrument track.
This issue I notice since Nuendo 4. Windows and Mac.
Now I´m in Mac with a Steinberg (Yamaha) UR44.
Thank you for your interest.