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I am developing on a Windows 2008 R2 Server, 64 bit. I am developing for SharePoint 2007, 64 bit.

My file structure has these two directories. I am trying to fix a solution reference in VS2007. Does it matter where I reference something, are these somewhat duplicate dirs, or how should I consider these two dirs?

A: 

The Program Files (x86) directory is for applications that are set to run as 32-bit, while the Program Files directory is for applications set to run as 64-bit, so, yes, they should be considered different.

Fredrik Ullner