What you read was correct. The register is an extremely complex and critical "nerve center" of windows, and I have never seen an automatic "cleaner" yet that did not eventually damage something. I have tested several. Most of the time it is just that some programs will suddenly not run, or don't run correctly. In extreme cases it damages Windows and XP will not boot. I use a scanner that searches for words that I type in, but I manually review and delete the entries so that I know what is being nuked and what is not. This works for me.
At this point, my suggestion is to run a Hijack This scan of your computer and post it in the malware forum
HERE.There is also a possibility that you have a baddie or two slowing you down, and that you have a lot of junk loading that you are not aware of.