Trying the same thing with Gboost running - crashed.
Trying to start the game by going FOMM - File - Run fose - crashed. Ran FO3MasterUpdate, everything went smoothly. Created the merged patch, put it last in the load order in FOMM, ticked it, closed FOMM. No errors are showing in the right panel, it says 'Background Loader: finished'. So I have deactivated and deleted my previous Merged patch.esp and I'm now setting up a new one. I'm trying the MasterUpdate/Restore at the moment.
I also tried running it with Gboost, same situation, crashed. It takes me to the Bethesda-screen and then it crashes. I tried to start the game by going to FOMM - File - Run fose, but it crashed at startup. Allright, so I've just finished downloading and installing all the mods I want.