In this patch I used both the two FX buses and noticed that, after project song being re-opened, the setting was not retained correctly until I opened the plug-in GUI. Dune 2 would respond with a short period of glitch and finally load up the settings.
Uploaded is two project files from Ableton and Logic. To reproduce the issue, start playing right after loading the project song; while it is making sounds, open the Dune 2 plug-in window, and notice the change in sound.
*EDIT: thanks for checking it out, glad it'll be fixed.