Realize that each time you get these things your entire security is severely at risk. You have to do something (even if it means switching Operating Systems) to stop yourself from getting them in the first place or eventually the results will be disastrous. Playing cleanup just isn't enough. As a webmaster, if the wrong thing gets in your system and you update your sites it could potentially mean infecting thousands of users or worse.
I'd probably reinstall to be safe. But if you don't want to do that make sure you are running those programs in safe mode. And are you sure the problem isn't an infected router? Don't forget to check to make sure it didn't set a proxy somewhere either. Sometimes these utilities will leave the errant proxy in place within the settings.
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