I hope it helps. I can't run the support tool because 3 of the 4 Windows 7 computers don't have NET 4 and I was unwilling to install it.
I did find this when someone complained about the notification of updates in the free version.
If you right click on the MB system tray icon, you will see "Start with Windows" with a check mark next to it. Click it to remove the check then click quit Malwarebytes.
That should stop the popups. If you scan, you do have to remember to turn MBAM off again.
Since last night (after 11 pm) one of my computers keeps telling me there is a new version waiting to be installed.
I was just at the forum and haven't seen anything about it so I'm holding off installing until I find out what version and if there are problems. So as of now, I have an annoying popup on my laptop! All the computers have v 4.4.4 from the end of July.