Mm, it's definately the mod. I restored my backup animations and changed all the Roman fs_s1_gladius skeletons back to fs_swordsman, and everything is back to normal. The non-modified units work normally again too...
SigniferOne, it's a brilliant mod and it's unfortunate that a problem such as this makes the game unplayable (since nothing works in battle when they're all confused), because I did like the mod. I don't care for archers and never use them, and phalanxes look fine to me--but I absolutely loved the accurate Roman warfare, and I was pleased to see Roman styles differentiated for once. I hope you can find a fix for this problem soon.
EDIT: Problem solved. I was a goofball and didn't upgrade to 1.2. Whoops.
That meant, of course, that I had to painstakingly re-edit every single change I ever made to most of the game's files. Fortunately I've the benefit of hindsight and I already knew what to fix, so that's good.