Below is a copy of part of my mods. I am showing just the NYGM related mods. On the download section Stiebler lists the correct sequence in which to load the mods here ...
http://www.subsim.com/mods1/nygm/
NYGM Tonnage War V2.5 – Stand Alone Version
NYGM3_New
NYGM3_6F
Hitman 1.2 Optics NYGM 3.2
IABLShipsforNYGM_New_Thomsen
3rd Flotilla Mod
Supplement to V16B1 (JSGME)
NYGM_HiRes_Submarines_3_6F
Stiebler4C_SubsFlag
Kapstadt Blockade NYGM3.3
Ahnenerbe WideGui 1920 x 1080 Final - FILES for NYGM v3.6D
Are you installing zip files into your Mods folder? You need to unzip the files before inserting into the game. You may want to reinstall a new copy of 3_New and 3_6F as you may have a corrupt files. Also try installing each one, one at a time. Install the first and start up SH3. If everything is working install the next mod and test SH3 to insure every thing is working as it should.
Good Hunting
FUBAR295