All right, I fixed it. Don't know what exactly was wrong, but here's what I did:
1) Roll back SH3 Commander
2) Use JGSME to uninstall all mods
3) Reinstall them in the same order
4) Launch with Commander.
For some reason, it works now. It means some files affected by mods were corrupted. Don't know why, because I changed nothing in game files for a week or so. But happily no re-install was needed, nor was my career corrupted... Mid-patrol saves worked too.
Thank you all for help
