If you're altering core files, they're binned for quicker load times. You either have to manually recreate the bin files, which there are batch jobs for, or delete them and have the game recreate them on startup.
OMG!!! I was thinking it might be something like this b/c I saw all the .bat files in the Tools folder at one point, but I'm extremely sarcastic and pessimistic by nature so I didn't dare get my hopes up lol, and I was/am still too busy working on my private mod to be able to stop and check them.
THANK YOU SO MUCH FOR FINDING THIS!!! Okay Stardock/Brad: I'm officially not mad at you anymore. *hugs* 
Just fyi guys, the reason being able to mod the Core files REALLY matters (well the reason I care about anyway - not sure if there are other reasons too heh), is b/c it allows you to use Mods in Multiplayer. You just zip up all your mod files beforehand like an official download version, send the mod zip to your friend/s, have them also Core install it, and THEN start a MP game.
In my case at least I wouldn't be playing GalCiv3 AT ALL if this weren't possible, and discovering it is the reason we came back to the game last winter after a 1.5-year break. 
