it doesn't show up when i try to enchant a piece of armor at the arcane academy any idea why?

My first thought would be that your item cannot contain the charge of a grand soul. Find a better item or better armor which you can imbue with the enchantment.

Allitems can hold any enchantments
On topic: This sounds rather wired, but is it possible that it is a quest item? There is at least 2 black soul gems thatyou can fill, but not use so maybe thats it?

You're talking the ones from the Cheydinhal recommendation? They would have to be handed to Deetsan to complete the recommendation, which would make them impossible to use at the University.

Is the armor already enchanted?

Anything that's already enchanted isn't in the list of items to choose. This question is why the one soul gem isn't in the list for that selection, and I believe the "quest item" answer is the right one.

Is it just tagged in the inventory as "Grand Soul Gem" or does it have another name that suggests it may be different? Can you drop it and pick it up again (quest items can't be dropped)?