Custom made armor will not show up properly in game. They appear to not be assigned to the correct body slots. I have a mod which had custom Mage robes utilizing vanilla models and textures. These no longer show up in game after I saved the mod using the lastest version of CK. You're character now appears naked even though the items are equipped. you can actually double equip Vanilla armor/robes while wearing my modified robes as they don't seem to be taking up the same inventory/body slot and any effects they have will stack.
Already been reported. This is a pretty serious bug, though, considering how many armor and clothing mods exist out there. At least 2/3s of the mods available for this game (3/4 counting the Edited Dialogue bug) are now completely broken.