Sounds as if you have a sysex message that resets to GM at the beginning of the sequence. Is there a system or global page where that is one of the options? I'm not familiar with the VA operating system, but I have worked with sequencers and there usually is some sort of command that will automatically reset to General Midi. I've had that happen to me and its frustrating to say the least.

That's all I can offer for now. Maybe Fran Carango or Donny (DNJ) could help. Good luck.