I had a somewhat similar problem two days back. I felt like experimenting and installed the english map names even though JSGME warned me it might cause problems. After that my game would crash at the load screen everytime I started a new career.
The old saved game worked fine. I reinstalled all mods through Commander but didn't help. Eventually after a clean reinstallation of SH3 and Commander everything is under control now.
Did you uninstall the game properly? I suggest removing the registry entries and everything before doing a clean install. I hope this helps you in some way. Good luck!
Edit:
Ahh Jimbuna beat me to it!