Obviously I can't speak to your situation specifically, but it is very common these days for people to have malware that was installed through an exploit that they've never detected - indeed it can be very difficult to detect a lot of modern malware without in memory analysis and skilled forensics. Signature tools and things like malware bytes are extremely hit and miss. OS X and linux are even worse off (at least with standard configurations) once something has done a remote code execution and gotten a privesc.

Poll a few people who do security work and ask them if they have acrobat or flash or the jdk installed at all, or running on pages by default. You'll hear about the same thing.

Even 5 years ago was a very different world as far as threats go.

I'd strongly suggest using an alternate PDF reader (apple, google, evince, sumatra) and using flashblock.