Install firestarter and have a look at the events and use the terminal to find out what application is causing it and if there is one you never authorize. Then you know.
Javadriveby does not need root privileges to harm your system. If java is old then well it will run. Normally you know by how much resources your browser is using. If the windows starts dimming down and web pages slow down then chances are its done something to you. Wireshark is ideal for spotting exactly what is going in and out of your computer so maybe look in to that if it happens again.