I think it would be a bit hard to tell speculate on exactly what is causing this without having your database. It could still be your Service Types, a database switch or it could be options on your ITMs; less likely to be an option on the ITM if this is happening consistently on ALL parts though.

I would like to illuminate that a single fabrication part is a wrapper of the various sub-parts that make up an Item. Very similar to having nested blocks. Each of these sub-parts are indeed referencing layers and styles which are all based on the CAD Types. I would go to the Database\Takeoff\Services\CAD Types\

Make some changes, go back to your model and run the REBUILDALL command to regenerate the layers. Rinse and Repeat until the problem hopefully goes away.... I think it is the most likely suspect anyway.