Originally Posted by Stiebler

Other problems fall into 4 categories:
1. Other mods that have also been installed onto this NYGM foundation.
2. Corruption of some of the game files in My Documents\SH3\....
3. Corruption of your basic SH3 set-up by mis-use of JSGME. (You have changed some files in your setup that have been added with JSGME, and therefore they have not been removed.)
4. Corruption caused by misuse of SH3Commander. (Useful, but not required with NYGM.)

Strategies for problems 1-4 above:
1. Remove non-NYGM mods from your mixture and try again.
2. Rename your My Documents\SH3\data\.... to My Documents\XXXSH3XXX\data.... This means you will start again with a completely fresh series of files, but you can if necessary recover your game-save data at a later date from the XXXSH3XXX\data folder.
3. Use JSGME to UNLOAD all your mods from your current set-up. At the end, you should be left with only the basic SH3 game files pre-dating the end of 2006 (I don't know about Steam versions, they might have later dates). Having established the integrity of these files, use JSGME to reload the basic NYGM components up to and including NYGM_2017 again. Test that this combination functions correctly. Then continue by adding your other preferred mods.
4. I have little knowledge of SH3Commander, so can't help much. Check the main SH3Commander thread. However, I recall that not unwinding past changes before starting new changes can cause a lot of problems.

Adopting the above strategies will certainly get NYGM running for you properly again, at least up to the NYGM_2017A level.