Whoawhoawhoa. Slow down. What mods? Which game (EAW or FOC)?
Things to check:
Are your mods in the mod folder?
Are you loading the right file with the right mod? (eg if you save a GC while playing one mod, you will not be able to open the GC in any other mod or in the original game).
If you have a whole crapload of files saved, try deleting some of them.
I need more information on the problem to diagnose it more specifically.