Not sure how long this has been an issue as I just started using ItemTracker this week but it appears to count most of my items multiple times.
For example, I made a Six of Cranes on my scribe. I have ONE of this card.
Immediately ItemTracker said I had two; one in bags, one in bank (despite the item never being deposited in the bank). I mailed the card off to my main for storage.
Upon arriving on my main ItemTracker now says I have FIVE of this card; two on my alt (bank + bag) and three on my main (two in the mail, one in bags).
This happens with every item and is really interfering with my crafting, as TSM thinks I have hundreds of each gem cut or enchant and refuses to craft any new ones.