Constant momentary alert popups - malware?

Hello all, I've tried to search past threads for some guidance on my issue but I can't quite determine what the proper nomenclature to describe what's happening.

This morning, I installed some software updates on OSX that required restart. IIRC, it was updates to Safari, HP printer drivers, and Java. I booted over to Windows for a bit and then back to OSX.

Now, regardless of which application I'm in, every 5-7 seconds a momentary alert box pops up and then instantly closes, stealing focus from whatever window I'm in for a fraction of a second, and perhaps eats a single keystroke or an open drop-down menu before the window gets closed.

This reeks of malware to me, since alert windows don't typically close themselves. Please let me know if I should post Activity Monitor screencaps or whatever else might be useful for more info, I simply don't know how to proceed since I've never run across anything like this in 8 years of OSX use.

I've disabled all Java runtimes, downloaded ClamXav but could use some insight on where to scan. If there's a place where popup alerts are logged, that would do a lot to give me something more to work with.

The alert boxes have the yellow alert triangle and seem to be in response to a process crashing. I'm now going to start just killing processes in Activity Monitor to try and isolate it.

UPDATE: I've removed all startup items from my admin account and the popup continues. I even log into another account that I've hardly ever used on this machine and the popup continues.

UPDATE 2: Finally pointed a 60fps video camera at my screen and got a frame of the popup. Do you want the application "java" to accept incoming network connections? Clicking deny... etc etc

Seems sketchy since I disabled both Java runtime environments hours ago. Blocking all incoming connections in Firewall has stopped the popups. However, I would like to get this process off of my machine. I am fairly convinced that it's not Java. I can't find java.app anywhere on my drive, so is there a way to reverse search for programs based on their name?

Run /Applications/Utilities/Console and peek around in the logs for anything strange. There should be something related.

Googling around with the alert message led me to this thread:

https://discussions.apple.com/thread/3804051?start=0&tstart=0

And to this blog article:

How to allow java in the firewall on OS X Mountain Lion | Tech Blog (wh)

I feel pretty confident that this will solve the issue for me. I'm running a repair permissions now and a lot of corrections are coming up in /sys/lib/frameworks/Java*. I'm going to leave this thread here though, since this is a tough problem to Google for and hopefully anyone else that develops it and finds this thread can get themselves to the answers.