I tried to post the save of a game I had been experimenting with but unfortunately it exceeds the file size limit, probably because I play on huge maps.
Since I typed this explanation before I realized the file wouldn't attach, I guess I'll leave it and maybe it can help in some way. In the army stack in the captured city of Caelistis I have at least one Greater Werewolf (a dwarven chariot) that is unable to take promotions, one Blooded Werewolf (a shadowrider) that is unable to take promotions, and at least one Ravenous Werewolf (originally an ogre, but with promotions I got it to level 6 and upgraded to stoneskin ogre).
I had a few other unusual things occur in this game, most notably there are two Alcinus units running around. One of them is a werewolf under my control, that for some reason must have spawned without being undead. I think it was under dwarven control when I killed it with Alazkan (also werewolfed) and was pretty surprised when it came under my control. I think it had no promotions at all, yet it was level 10. The second Alcinus (I guess the first one really) was behaving as normal, and actually passed into my control as well via his normal death behavior. This is something I'd never seen before, so I have no idea what might have caused it.
Anyway, sorry that I can't post the file. I have a hard time believing that I'm the only one with this werewolf problem. I know it was endemic in the game for a long time, I even think Valkrionn mentioned it in passing in some thread somewhere, but even then no one mentioned a fix of any kind.