I have run across strange behavior, somewhat similar to yours. The best I can do is insure that I don't check certain selections on the Registry Clean Function. See my post v.618 Registry Unused File Extensions, clicking 'Unused File Ext' causes programs to fail" back on 14 August 2008, one page forward from here.
When I run the registry check for errors, and check the "Unused File associations" some of the obviously good File Associations are apparently deleted and in particular the .msc will not run so, for example, Diskeeper will not run. The same for .htm and a few others. I can either restore the backup.reg or I can run some of the file association entries that are available from Microsoft MVP's to fix the problem. The problem also extends to "missing shared DLL's"
Perhaps a comparison process with what should be there in the analysis "rules" is not quite understood.