Why does a second run of the program still find a few dozen invalid entries?
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Some programs save working information in the Windows® registry every time they are run. That information may be information such as 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 has the saved link to the file in the 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 a lot less invalid references than you had before a first clean. For example, 5-10 instead of 700 invalid entries. To avoid invalid references' accumulation in the registry we would like to advise you to clean registry with Registry First Aid regularly.