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I use Microsoft Security Essentials for my virus protection but I also run scheduled scans with Malwarebytes and Spybot Search & Destroy. Should I disable the MSE realtime scanner when these other scans happen? Will they conflict?

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No, as spybot scans files your active AV software is watching also, if spybot scans a file and does not have it listed as malware but your AV does, it will catch it, I have seen this a few times while scanning PC's using Spybot, MBAM, and SAS.

No single AV or scanner has 100% of malware signatures in their detection dat files, another reason to use more than one on demand scanner, when Spybot is done run MBAM, then when its done run SAS

What you don't want is 2 active AV software's installed at the same time, Norton and McAfee for example.

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I found a good article that may be of help to you. From what I can gather from the link, it's totally ok to have multiple virus/malware scanners on your computer. Having them scan at different intervals is fine it's just the "real-time monitoring" that can cause issues.

http://www.freewaredaily.com/why-does-having-more-than-one-virus-scanning-application-on-a-computer-cause-a-conflict/

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The reason you may want to disable your real-time scanner while running an on-demand scanner such as MBAM or SSD is to speed the scans by the on-demand scanners.

However, while you are running such dedicated on-demand scans with real-time protection disabled, you'll be open to infection and/or attack, and so disconnecting from the internet during these scans can be a good idea.

Generally, a real-time scanner can co-exist with on-demand scanners without too much issue or conflict. As others have said, the real problem, the absolute no-no, is to run two real-time scanners simultaneously.

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