Sure you had an infection?
It doesn't sound as if you actually had an infection. It sounds like you had a registry error with the installed executable for MBAM.exe.
In the future, you might want to try running SuperAntiSpyware Portable (or even just the regular SuperAntiSpyware, preferably from Safe Mode with network support) if you can't get MBAM to launch as it should. And once you've completed a scan with SAS, try MBAM again. And if MBAM still doesn't work, uninstall it, grab JV PowerTools Lite 2011 and scan the registry with first the default safe settings, and if that doesn't fix the issue, again with the registry scanner in the second most aggressive setting.
Run Malwarebytes as soon as possible during boot...
Some viruses are very clever at spotting trapping and bypassing Malwarebytes.
I've had to use MBAM once and it really saved my bacon. And due to restrictions by my IT dept I couldn't use safe mode. I managed it only by clicking its icon as soon as it appeared during the boot before the virus/trojan had a chance to bypass it. I think I remember having to reboot a couple of times before I got my clicks in ahead of the virus activity.
I now keep a copy of MBAM on a memory stick just in case. Along with a copy of RKILL which helps a bit.