I have had the same issue, at the same time, as you have. Malwarebytes continues to disappoint me ever since the move from Ver 2.x to 3.x, I have had nothing but one issue after the other. I now no longer recommend to clients, family & friends their products unless they have spare time on their hands to sort out the issues they may encounter. It would appear to me that they no longer conduct alpha and beta testing and just leave it to the end user to report the issues encountered and expect the end user to share their fixes in the community forums.
Anyway, back to our shared issue, I have had to do the follwing:
1) Download the free version (again).
2) Go searching for the original email/invoice from CleverBridge AG (who sold me the product) and locate and re-enter the original id key and licence key to the Subscription Details section in the 'My Account' tab of the Malwarebytes programme.
3) If you are reading this Malwarebytes, please test these upgrades/updates FIRST before releasing them onto the unsuspecting end user. Very disappointing that your processes appear to be getting worse rather than improving the end user experience.
I would like to say it was a pleasure in trying to assist this user, however it would have been unnecessary if you had bothered to check your processes first.