using VC6 and VA 1541 I still cannot reproduce this.  Can you try the following code and see what you get.  I have added:
#define FIND_REF_TEST_DLL_EXPORT _declspec(dllexport)
class FIND_REF_TEST_DLL_EXPORT testFindRefExportedClass
{
    // test - Find References on this function finds 2 references
    void CppFileTest();
};
to the header file and:
void testFindRefExportedClass::CppFileTest()	{ }
to the cpp file.  When I trigger Find References or rename on the class name in the header file I always get 2 references.