Could you check the following registry key: HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\hivelist, is all registries are placed in system32\config folder? (especially 'software' one).
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Could you check the following registry key: HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\hivelist, is all registries are placed in system32\config folder? (especially 'software' one).