Yes, malware is a broader term, suitable for most uses. I didn't know your or any other reader's level of knowledge, so for those who didn't know, I made that clarification of terms. Under the hood of it lie terms like Adware, Crimeware, Spyware, Scareware, Grayware, Viruses with subcategories and what not.
Nevertheless, it is quite hard to draw borderlines for wanted or unwanted programs. Of course, for us gamers any redundant programs can be considered as PUP's (Potentionally Unwanted Software), but for an average surfing Joe they might be of great help. That is why you can't trust just one security software. It is good practice to have an antivirus accompanied by a firewall running in the background, but as your example shows, it pays to do a malware scan with a dedicated program every once in a while. Many antimalware programs can be run in the background just as their antivirus counterparts, but that would highly possible cripple gameplay. It would definitely do no harm either to run an on line virus scan just to check your installed antivirus hasn't been bypassed.
I work as a computer repairman for households and I must say I have seen all available antivirus programs being bypassed, both commercial and free ones. Often the infection has started by clicking a pop-up warning saying "Your computer might be at risk". And just to make finding the source more difficult, some malware don't start doing their thing at once, they can wait several hours or until next restart before they try to install something into your computer. That's why I don't believe AdobeReader's autoupdate was the culprit in your case. It might have been a catalyst, though, if you had a vulnerable version, or the malware might have been waiting for any install procedure to piggyback on it. Otherwise updating through inside the program should be safer than downloading updates from a third party source.
