The only time I've gotten less than grand souls in black gems was when I sorta broke the blackened Azura's star via console shenanigans. They're supposed to only work for holding human/daedric/etc. souls, which are all grand, but it's possible the game will bug out and dump smaller souls into your black gems when it shouldn't. This is Bethesda we're talking about, after all.
Sidenote, I just finished my fully tricked out legendary/double-enchanted Ebony set (because screw Daedric) which I have dubbed the Shadowguard set for my new paladin character: 2-hand weapons, heavy armor, restoration, smithing, enchanting, and only as much archery as is required for shooting down dragons, pretty much. Unfortunately patch 1.2 has sorta fucked this character over against mages: being a heavily armored, short-range character makes her fodder for magic damage as long as resistances aren't working. And yes, they are screwed up: I was getting one-shot by an arch necromancer's frost spell when I'm a Nord (50% frost resist) wearing two magic resistance items (44% resistance to all magic).
Dis not cool. :|