To be honest I do not run any antimalware scanners myself, but I seen first hand the effectivenes of MBAM (and also SuperAntiSpyware - SAS which was the main flavour before MBAM) in the malware forums and both are great tools to have around. The only thing I do not like about MBAM is that in the paid version they have an IP blocker which has resulted in a few IP's being registrered"Bad" when they are not. I agree that MBAM does have its false positives but I would'nt class it as "many" which makes it sound a regular occurrance, I feel no scanner is not prone to the odd false positive. Usually Bruce is good at adding items to the whitelist but I cannot say if the software you mentioned have been whitelisted or not.
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users should be aware that Malwarebytes is not an anti-virus scanner
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%100 spot on, many people forget this and rely on it to run it as their main security application, it should be complimented by a good antivirus as you mentioned