I know this is a bit old, but I thought I would provide another tip. In my situation, I inherited this application that I had to maintain. The VS2008 project came with the same string in C/C++->OutputFIles->"ObjectFIleName" and "Program Database File Name" (for both platforms Win32 and x64). So when I built Win32 platform, it built fine, but when I tried to build x64, I got the error:
\Debug64\Objects\common.obj : fatal error LNK1112: module machine type 'X86' conflicts with target machine type 'x64'
Obviously, both patforms were storing common.obj at the same location, so when I tried to build x64, the linker took the existing object file, which was x86.
To fix I just replaced the existing string with the macro "$(IntDir)\" for x64 (no quotes), and made sure that the macro resolved to the correct path, as in the rest of the projects. That solved my problem.