Some registry entries depend on others. If Registry Healer finds errors in some entries, it can't exactly detect that the dependent entries are invalid. Only after the first correction it can validate the dependent entries. Also, there're some complex registry entries that consist of several parts, like a list of file paths. For many registry entries correction for a part of a complex entry depends on the previous part that should be valid.
So, if one or more parts are invalid, Registry Healer will show only one. After correction, on the second scan it will find next invalid part, then next and so on until all invalid parts of every complex entry is corrected. It is suggested to do several registry scans and corrections one after one.
Some programs save working information in Windows® registry every time they are running. That information may be like paths to currently nonexistent files. For example, you've created a new file in WordPad, saved it into a temporary folder and then moved it to your documents folder. But WordPad have saved link to the file in temporary folder as a recently used file. So if you have successfully cleaned the registry and then were working with your computer, after restarting you may get some invalid registry references again. It is normal situation and there's no reason to worry. The main thing is that you get many fewer of invalid references than before a first clean. For example, 5-10 instead of 1000 invalid entries. To avoid invalid references' accumulation in the registry we would like to advise you to clean registry with Registry Healer regularly.