I had this problem as well, when I was adding a bunch of units to my game. I only had about 10 or so added, but I got that same message. I had also copied the original civ3mod.bic, in case I somehow corrupted the one I was editing, I tried to replace the corrupted one, and, lo and behold, my new one was corrupted-- somehow the problem carried over. So I too uninstalled the game, then reinstalled it, and got the v 1.17 patch again, and now it's working just fine, and I'm still making units... It sure would be nice to know what exactly causes this problem though, as I really can't imagine what I did before.
Maybe it will be addressed in the next patch. Anyone have any idea when that comes out by the way? There was some talk about it a few weeks ago here on civfanatics, but no word since.