Spyware has some of the same issues virus software used to have when installing programs. SpyBot is one of my favorite antispyware programs, but it's definitely counterproductive to run spyware programs simultaneously. While it's understandable that you may need multiple programs to get full protection (I use both SpyBot and Ad-Aware), you'll probably need to take a more hands-on approach by unloading one program and running the other, then later in the week reversing the process, unloading and reloading as necessary.
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I've also started noticing on the forums that users are having problems with SpyBot turning off programs the user needs, like Active X and Flash. Your gripe, then, may solely be with SpyBot. If SpyBot is the only antispyware application you have running and it still thinks some of your customer's needed programs are spyware, you may need to run it in a reactive, manual mode only -- load it to run a scan, then unload it.
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