Ok, so here is what I did.
I dont have the new repair tool I am making for the package files done yet, its a lot of work. BUT I did finish the code to add the cat files back to the catalog database.
So I just put out Windows Repair v3.1.2.
Go grab it, and then open the Pre-Scan tool. There you will see a new check box to add the .cat files. Put a check on it and then run the pre-scan. The scan will be slow, because now when it goes through the packages files it will add all the .cat files it finds to the database.
Let me know how the scan looks after that and lets see if that fixes some, hopefully all, of the bad signature mum files
Shane