I'll also add that there are times when the behavior described by the OP is entirely normal. If you let it go for a while, and it goes away, I would not get too exercised about it.
I've had this issue intermittently and it usually irons itself out and stays ironed out for months until the next time, when it irons itself out again.
It is also becoming less and less clear what Malwarebytes "really is." They are introducing realtime scanning that is quite congruent with what anti-virus and/or security suite software does and this was not always the case. Since I use strictly the on-demand scanner there is no conflict, but I'm not so sure there mightn't be these days given the architecture changes to the latest version of Malwarebytes and if you use the free trial or paid version with realtime scanning. Their marketing isn't helping matters, either, with the "makes antivirus obsolete" tag line.
Brian AKA Bri the Tech Guy (website in my user profile) - Windows 10 Home, 64-Bit, Version 1803, Build 17134
In a modern society where everyone thinks their opinion deserves to be heard nothing annoys me more than individuals who mistake their personal preferences for fact.
~ Commenter TheCruyffGurn on the The Guardian website, 8/13/2014