I've encountered a strange bug, sometimes items disappear from my inventory.

For example, a Retort disappeared from my inventory list, but I still had it when I made some potions. Likewise for some equipment ( a chest and a ring dissapeared once ), they don't appear in the inventory, but their armor rating is added and I'm wearing them! They come back though, but I can't find the reason why they disappear or come back.

I use DarkUI_Darn, so perhaps that's the cause?

How many items do you have in the inventory? I think this happens when you have too many items in one container (inventory or other containers). They are still there, but they don't show up in the list. Remove some items from your inventory and put them in a chest.

IIRC there's a limit to how many things can be in a container or your inventory before some don't show. I'm overburdened way before I get to that stage, but you may have exceptional strength or a lot of weightless items.

I've seen this happen with containers instead of the player, but I'm guessing it'd work the same way. If you have tons of items, or a ton of items repaired to 100+ repair, then the number of items needed for this to happen goes down.
I'd recommend using http://tesnexus.com/downloads/file.php?id=9835 mod to sort them out into containers(first you have to read the book, though, and if you can't do that...). I use it for sorting my massive loot collection, which is mostly pack rat junk. But I'm guessing it'd help quite a bit. Assuming you spread the items out enough, anyway.

Well I do have a gigantic amount of different gems in my inventory, as well as a gigantic amounts of ingredients. I'll remove or reorganize them. Thanks for the tip.

If it's just ingredients, then you might want to just use COBLs alchemical sorters(or http://tesnexus.com/downloads/file.php?id=25436).