I'm sorry that you're experiencing these issues. I'll run some tests and get back to you as soon as I can.
In the meantime, shutting the H9000 down when you're done for the day and turning it on before you begin working could help.
Could you use the standalone instead of the VST, and automate Emote's Functions with a MIDI track in Studio One?
We will be adding VST3 support in the near future, which I'm hopeful could resolve your issues.