Originally Posted by
Hiruke
You're only getting reputation from the Grand Company that your Free Company is currently allied to. You can switch your Free Company's allegiance to another Grand Company if you so choose, by speaking with the OIC rep at the GC in another city (e.g., if your FC is allied with Twin Adders, you can go to the OIC in Ul'dah or LL to switch to that one instead).
Once you change allegiance, you should be able to gain reputation with you new allied GC.
I'm not sure if this resets your FC's rank, or if it only affects reputation gains (or what those mean, if anything, outside of building FC Rank). You'll also note that you can only do certain actions, like put crests on your gear, at the OIC in the GC hall for the GC your FC is allied with.