I've seen this thread and, in particular, I am aware that some are concerned about slow scanning following their MalwareBytes upgrades.
What follows maybe a bit of a longshot, but here goes.....
Well, I'm still using the old version and I've also found the scanning slow just very recently. But I've discovered that it is down to something that I have done (and maybe the latest MalwareBytes uses as well).
I run Windows 7 and got fed up with the User Access Contraol permission dialogues that I got when running a number of applications. So just recently I followed the instructions here: Seven Forums link
It's only this evening whilst running a MalwareBytes scan that seemed to be taking ages that the penny dropped.
I was already aware that in the normal course of creating Scheduled Tasks they cannot be set above a certain priority (and I'd fixed another home brew application some time ago that had suffered in this way). So I tried the same with MalwareBytes and hey presto - much faster (down from just over 1 hour to 18 minutes).
Now, what I don't know as I don't have the latest MalwareBytes (and so this is a bit of a shot in the dark) is whether the latest MalwareBytes installer has used the above-mentioned Scheduled Tasks "trick" to circumvent the UAC prompt.
So if someone can have a look in their Scheduled Tasks and see if MalwareBytes is (now) in there (and also a giveaway is that in running MalwareBytes it no longer invokes the UAC dialogue).
If this is the case, then the way to up the priority is to Export the task (as an XML file) and edit the priority therein and then delete the existing Scheduled Task and Import the edited XML file. I upped the priority in mine from 7 to 6 (which should be sufficient - you don't want to make it too high as it may interfere with critical Windows processes).
Also a quick further point on priorities. Originally I had assumed that if nothing else (much) was running, then even a very low priority task would get all the CPU etc. that it wants. It seems that with Windows this is not so. So to get things running at a reasonable speed (if using SCheduled Tasks) the priority must be set to at least 6.