I used Regseeker once for a registry cleanup and a couple of days later it was clear I needed to do a restore to undo the problems it caused.
It is still on my system for Registry searches but it won't ever be used again a cleaner.
To a degree I agree with Alan on this, RegSeeker is a very powerful tool and not a very user friendly one with no help file or references, etc. So you can't take it as gospel and have to check each entry that you intend to remove, rather than simply select them all and remove them. It does back-up any changes if you didn't deselect that option, so to a point there is a way back.
I have been using it for years without problem, but you shouldn't stray from the Green entries and even then check them, this obviously implies you have to have a reasonable understanding of the registry. This no doubt Alan has, so it just goes to show the registry isn't a playground and you have to have a good back-up and recovery system to recover form registry problems.