I have a Visual Studio 2008 project that has a reference to a dll. I removed the reference to version 1 and added a new reference to version 2. The project builds successfully, however when I analyze the project dll after it has been built in Reflector I am seeing that it is holding onto two references to the same dll – version 1 and version 2 are both referenced.
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If you look at your project file in notepad, can you see both references in there? You may have to scan through a bit of xml to find them… If so, you could manually remove the old one and resave the project in notepad.