Did you enable NYGM before trying to Patch to 1.4b? If so then you need to follow the reinstall directions...
Ok, first let's find out which version of SH3 you have.
Download & DVD?
US or European?
Then make sure you have the right patch from here -
http://www.silent-hunteriii.com/uk/updates.php
If we have established that you have the right patch version, My next suggestion would be to totally uninstall SH3.
If you use SH3 Commander then make sure you have 'Rolled Back' first.
Process:
1)Unistall SH3
2)Delete Program Folder for SH3 + My Docs Folder for SH3
3)Search the registry for SH3 leftovers. (optional but recommended if you are happy doing this)
4)Restart your PC.
5)Install SH3 V1.0
6)Apply Patch 1.4b
7)Start SH3 to make sure it works.
Providing it works....
8)Install & setup JSGME.
9)Copy/Enable NYGM via JSGME.
This should get you up & running.
Just ask again if you are having problems.