Your problem is that you have installed too many things to quickly.
Heres what you do:
1. Freshly install Bridge Commander
2. Run once to make sure its working
3. Install the Bridge Commander Patch
4. Run the game to make sure it is working
5. Install BCMP to get the Foundation scripting installed in Bridge Commander
6. Run the game to make sure it works
7. Run BCMP once (stay away from the 'File Checker' in BCMP) to make sure it works
8. Install BCMI and make sure it points to the loaction where you installed Bridge Commander.
9. Run Bridge Commander once to make sure everythings OK.
10. Install NanoFX 2. NanoFX2 doesnt work in singleplayer.
11. Run Quickbattle mode in Bridge Commander to make sure NanoFX2 is working.
12. Have some fun blowing those romulans into space dust.

13. Let me know how it turns out.
The thing about Bridge Commander is that you have to run it atleast once after installing any mod into it to make sure it all works.