Problem with malwarebytes version or actual malware?

Initially i made a topic in the software section because i reason to believe that malwarebytes has had bugs lately in its new updates.

Topic- http://forums.majorgeeks.com/showthread.php?t=275874

I havent really had any issues with my computer being slow,crashing, or viruses lately. Just some minor adware which is easily removed and doesn't cause problems.

Recently when my malwarebytes updated it said it found trojans but i since i have been having issues with the software in its recent updates, i didn't want to let it remove or quarantine said files because it they were in windows and i didn't want to have problems with my OS.

Last time it ran a scan a sibling of mine let it remove or quarantine a file/program it detected which i had to reinstall because it wouldn't work anymore ( software was something called rebox.net its a converting software).

A couple of updates ago, when malwarebytes updated and i ran a scan, it came up empty and clean but when it tried to close the program i got my first BSOD in this pc. The following week after that when i updated malwarebytes once again, it did the same darn thing after using the software ( hasn't done it anymore though).

Anyways i ran some scans , and i just wanted to verify if i actually have something or if its just malwarebytes causing issues.