'... weird pdf popup' is a bit vague. If you can include a screen capture that would help, or at least write out what the popup is stating. Also, is it just happening at random times, or only when you're using a web browser or some other specific app?
Keep in mind most serious exploits will occur without actually notifying you about their presence. Something like an actual keylogger won't advertise nor reveal itself, it's purpose is to steal your keystrokes covertly.