Hm, sounds like the game doesn't find the mod...
First of all: Why don't you use the launcher?

It should basically detect and install all files to the right directories.
If you have the steam version, you just need to activate the corresponding option in the launcher and it should work.
In your FoC directory (the one where the
swfoc.exe lies), is there a folder called
Mods, and does it contain a folder called
Stargate? This Stargate folder needs to have a
Data folder inside.