I have been using Regseeker 1.55 under XP for years with no problems. My two sons have Windows 7 and when using Regseeker it shows up literally thousands of registry issues. But if selected and deleted (with backup) they still appear when the clean process is run again.
It seems as if there is no one at home at Hoverdesk although their website is still giving downloads of their software.
Their user forum seems to suggest they abandoned ship.
Are you running the program as an administrator? Running it as a standard user gives only read-only access to the registry.
Generally, using Regkeeper on a new version of Windows isn't a very good idea either. If you're looking for a system cleaner, try Piriform's CCleaner, it seems to work for me. Don't want to post a link here to avoid being accused of spamming, but Google will turn up a good few results on the program :-)
Problem solved. They had a similar problem with Spybot S&D. Their forum said that even if the user was an administrator they had to right click (instead of left double click) and 'Run as Administrator'. That solved the Spybot issue and when tried also solved the RegSeeker issue.