Yeah, I tried RegSeeker way back and it stopped various things working. I decided that it was far too ambitious (like RegScrubXP) and dumped it. You have to watch these things like a hawk or accept the possible consequences.
I appreciate that many folk say they have had no problem with registry cleaners. Unless you are lucky enough to notice a problem very soon after using one (as I did in this post) then you never really know whether having to fix a software problem was due to reg cleaners or something else. Few people can claim to have had no software issues on their machine and the reason is not always easy to decipher.
One of the things to be aware of is that often programs insert registry entries to be used later. These have no value so are reported by reg cleaners. For example, SuperAntiSpyware has a registry entry pointing to a Quarantine folder which only arrives when a virus is found. If these things like this are removed, when they are required the program might get lost, requiring re-install.
I've also had issues where reg cleaners do not save the backup entries in reverse order, which can lead to registry entries remaining missing even after undo.
I do have some very mild ones as diagnostic tools but even these I watch very carefully. The only really safe ones are those that just show all names of software manufacturers and programs, so you can see anything that has stayed behind after uninstall. These are quite different from those which churn out wadges of alleged invalid entries.
some other bloke...