Hi DauntonHH, this is not normal behavior. The H9 should boot up ready to go. You mention you’re using it as part of a MIDI rig. Is it possible the controller is sending a message to increment or decrement a preset on startup; does this issue happen when the H9 powers up by itself without MIDI connected?
My suggestion would be to conduct a factory reset. Before you do, make a note of any system settings (MIDI programming, Routing, Aux switch mappings). Also, for good measure, backup your pedals preset list, if it’s customized. Press & Hold the right ftsw and Hotknob button while powering up the pedal. Let us know if this fixes the issue.