Wierd...
I have this for my legionary cohorts and it perfectly works
Code:
skeleton fs_javelinman, fs_s1_gladius
Did you make a backup of your original files ? You could retry to play a battle with them, just to make sure the problem comes from the pack. Though I don't recall of people getting troubles using it when I released it last September. All of them used it on mods built on RTR, just as RTR:AE.
Also check this thread, there may be some useful info. Honestly, that's the first time I hear of such a thing happening.