When doing the malwarebytes scan are you choosing full scan or smart scan? It is very odd that it won't pick up on the trojans/malware in your other users folders.
First, make sure you update it. There is an update tab. I have had it update to a new version within an hour, so always update first before you scan. Try doing a full scan and make sure every user is chosen. That should find something. Remove what is found and let it restart.
If that doesn't work, unplug/disconnect the internet and boot up safe mode. Then run a full scan of malwarebytes from there. Again, remove any trojan/malware found and let it restart.
Also, if it finds something, I would suggest going here:
http://support.kaspersky.com/viruses...?qid=208280684
Download that TDSSkiller software and run it. If it finds something, it will get rid of it 99% of the time. If it is still happening after the tdsskiller has run, post back in this thread and I'll give you some more links and help if I can.