I have suffered this bug several times. I cannot tell you what causes this, but I can share with you my working solution.
I have moved the entirety of my Titan Quest folder (the one that contains SaveData, Custommaps, Working, etc.) and moved it to the desktop. Then, I launched ArtManager, and it initiated some process. Let it go. Then, take back your folders from the desktop and move them back to their original location. This should fix the issue for the next mod you will create.
However, I have no idea the issue will be removed if you play on an already existing custom map.