Check the description of a commander with afflictions, then choose "fatigue". You'll see current age and maxage in there. If current age is above maxage, the undead are suffering from their ancient bodies crumbling down. It could still be a bug, because Ashen Empire undead are supposed to be pretty tough bunch.
If they aren't old, Burden of Time probably causes random afflictions. In this case, it is most probably a bug.
I've used the same strategy before in SP. That is, LA Ermor casting Burden of Time, and either something has changed since 3.00 to make the spell affect undead (wrongly) or I was especially lucky when using this in the past because I do not remember such serious problems afflicting my undead under the spell.