A little research lead me to believe that Windows 7 run 2 distinct registry. One for 32 bit programs and one for 64 bits programs.
It might be that the auto-updating registry file is not updating the right registry (in this case it would be updating the 64 bits registry), leading to the same initial problem as the OS is unable to find the required marks in the right registry...
Now I'm no expert in Windows 7 or any other OS after Windows XP... But it would make sense to me for Microsoft to push their 64 bits operative system first and thus make it the default registry.
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Source of my findings)