I am having a similar problem with Visual Studio 2013.
Yesterday after windows 7 update when I try to compile any project I get:
"Error 2 error C1041: cannot open program database ''; if multiple CL.EXE write to the same .PDB file, please use /FS E:\CProgs\GenEdit50Cust\GenEditG20\stdafx.cpp 1 1 GenEditG50" The project name and folder changes when I try to compile another project but I still get this C1041 error. I tried adding /FS and it has no effect?