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I can reproduce this on 3 seperate machines. It seems like ReSharper's configuration for VS2003 and VS2005 are stored in the same file and they keep overriding themselves. I notice the problem occurs when I have VS2003 open then I open VS2005 so now I have two versions of VS open. If I exit VS2005 then exit VS2003 then reopen VS2003 the color identifier checkbox is unchecked.
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Exiting VS2003 and opening VS2005 and enabling color highlighting in VS2005.
Existing VS2005 and reopening VS2003...now color identifiers are off.