Thanks for the reply John.
I found that if I were to remove the default values from the Debug Settings Panel>Language Settings>C/C++ Language>Prefix File for both the Debug and Release targets, I was able to compile both a Debug and Release version free from the Hotsync problem described in my original post. I do not know why this is so though.
This sounds like a problem with your precompiled header files... that's pretty odd, as I'd expect a bad PCH to just cause compilation to fail. Perhaps one of the debug flags is introducing code into your program that leads to global usage.
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