So, here’s the deal – be aware that I spent two hours of a Sunday for this. :)
If the Mod Organizer is used to start Skyrim, a Windows function to obtain the version of a vital – one could say THE vital Windows system DLL, which is used by each and every Windows program – fails with a “file not found” error. That is obviously nonsense, as the DLL can be loaded just fine, otherwise Skyrim wouldn’t even launch. Due to this vorpX operates in the wrong mode, which in the end causes your FPS loss with Mod Oganizer. My guess would be that the program messes with DLL search paths, but that’s just speculation.
I have now implemented a fallback method if something like that happens for whatever reason. For me it fixes the Mod Organizer problem, so there’s a good chance that it will work for you too. Will be in the next vorpX version.
IMPORTANT: The fallback may cause other problems, not work at all on your PC or kill your cat, so please consider it totally unofficial and absolutely not guaranteed work!