I found another Item on the game and ATT is not marking it as Collected.

Name: Cookie's Tenderizer
Item ID: 5197
Got it in: Dungeons and Raids > World of Warcraft > Deadmines > "Captain" Cookie
Equiped as Mace

Share Visual with:
Name: Tenderizer
Item ID: 86558
Equiped on Left Hand

Did you try a Shift+Click on the header to force a refresh? Currently both are checking off for me (Completionist mode so I physically have both)

Yeah I tried, I use Debug Mode. Cookie's Tenderizer is in my inventory, but ATT don't detect it or something, I tried a Shift+Click

Does it have the 2hr timer or anything? That'll cause it not to show up too.

No, its soulbinded already

http://www.wowhead.com/item=5197/cookies-tenderizer
http://www.wowhead.com/item=86558/rolling-pin

these items cannot be transmogrified.

That is correct they can't be transmogged, but you can learn their appearance and is stored in your wardrobe.

Had some people test it in our discord.

If you Shift+Click on the header then it shows it as learned.