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But there are times that it will affect the installation of a newer version of an older program that's been uninstalled and the registry keys not removed after uninstallation. I agree that having unused keys in the registry is not usually harmful to the computer in any way. Who told you that yop should be messing with teh registry?
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Not that CCleaner is bad, just that you shouldn't use that part of it. MS explicitly recommends against it, and for good reason. Do not, under any circumstance, ever use so called registry cleaning software.
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