[Quicksilver]

Malware Bytes is more focused on anti spyware so it will report cookies as an infection. (Not sure if this was your case) Cookies don't do anything except let websites identify you as you browse the web. There are privacy issues but it doesn't compromise the computer.
Also if you take any computer that has been touched by some sort of malware and run it through multiple scanners each one will find bits and pieces that the other ones didn't see. It isn't a big deal. The only important bit is to stop the bad stuff from running.
That being said: Malware Bytes is an excellent product but it is more of an antispyware product as opposed to an antivirus product.

Just as a general point: Any of the antivirus/security software supplied by an ISP is junk. (AOL's is the worst.)

If you want a real testimonial for an antivirus product ask what they are using at your local bank. If they are a large bank you know they have put a huge investment into making sure they are covered and that their protection software doesn't create problems. If they have a security breach they are accountable to multiple local, state, and federal agencies. They don't mess around and they don't guess.