hmm, just noticed that when attacking a city. Ok, you didn't mention that.
(I've worked as a game tester for awhile, so this comes kind of natural to be picky...) But, it has to be a mod, since the elephants have a gazillion hit points. Are you sure the Elephants weren't modded to have invisibility? Also, I just moved a Catapult out of Dehli onto the hill 1 N of the mountain that's 1 NW of Madras, and it says that it can't attack. So, the unit IS there. I'm guessing you used a mod that made Elephants have a lot of hp (999?) and have invisibility.
Looking at the Tech Tree, War Elephants come with... Advanced Flight???
Dumbo, perhaps?
BTW, I just retired from the game, and the correct score WAS in the hall of fame, so that's an indication that it's a normal save file. Maybe the save was corrupted somehow?
Did you, by any chance, mod (or download a mod for) your Civ3mod.bix file? (just covering all the bases)