In win7 with the system locale in Chinese, it can be reproduced in VS 2005 and VS 2008 by adding a non-ASCII(eg: 0xa9) character into comment or license header of a source file.
It seems that cl.exe and vs debugger haven't processed non-ASCII characters in the same way, so they got different MD5 checksums.
VS2010同样如此，并且有时候可以有时候却神经病一样不行！