Did you get any resolution to this problem? I am having exactly the problem with quite a large design.
I have found thta it complains about the 3D extruded model on top assmembly SM, top courtyard layers etc stating that "Model2D.Roatation =360 on PCB and 270 in Library.
I have made a test design and place a few components direct from the library (MySQL parameter library with standard Symbols and Footprints Libraries files - no svn) .I run the Tools-> update from PCB libraries and all is ok. rotate on of the parts and run update again and then get the error. Allow it to make the change but error doesnt go away.
I have tried this on ALtium 10 and it doesn sho the problem - however, on my large design opened in Altium 10 once I get to the end of "matching components" it just bombs out with an error "Access violation at address 095c7af0 in module WorkspaceManager.DLL. read of address 0000000 at 095c7af0 - Exception Occurred in Document Options.
Any help greatly appreciated.
Nigel