Malwarebytes doesn't deal with rootkits well. It also gets targeted and disabled by a lot of viruses and malware. Spybot is pretty useless for the past few years.
First goto My Computer, right click on the drive, and goto properties, tools, error checking, and check all the boxes and run. If prompted to schedule disk check with restart, do so and reboot and make sure the check works.
First, run Combofix.
http://www.bleepingcomputer.com/comb...o-use-combofix
Get DrWeb CureIt to deal with any virus/malware and to detect rootkits.
http://www.freedrweb.com/?lng=en
If there are rootkits it cannot deal with, use GMER.
http://www.gmer.net/