This worked for me in Win 7: First, turn off any other anti-virus programs you might be running. (In my case, MS Security Essentials)
1. Right click the MBAM systray icon.
2. Select "Quit Malwarebytes." This will cause the Windows Action Center to red-flag your anti-virus programs.
3. Click the flag (Action Center) and select "Check Anti-virus programs. This will cause a pop-up to appear listing the status of your anti-virus programs.
4. Select Malwarebytes.
5. Click "Turn On." Wait a few seconds.
The big MBAM systray pop-up telling you to turn on protection will probably still show up one more time (It did for me), but if you open MBAM BEFORE clicking "Turn On" you should see that all the layers are, in fact, on. So you can simply X out of the pop-up without clicking anything.
Both these issues (Not starting all protections, and the systray pop-up) are BUGS that I'm sure MBAM will get worked out, but it is annoying and concerning.
Note: If you don't turn off your other programs before starting this list, the Action Center won't flag the problem and you won't have access to the Windows feature in step #2. However, after you've gone through all the steps, and MBAM is fully working, you can turn your other programs back on without it changing MBAM's status. At least that was the case with MS Security Essentials. If you're running something else you'll have to see for yourself how it affects MBAM.
Good luck!