I'm guessing at the cause here. Here's the story so far. I have been setting up my HTPC using Ubuntu server and XBMC. Everything has been working great. Slowly adding more services. Have an FTP, torrent, SSH, Crashplan backup client, and Samba server all running great. Yesterday I decided to try a subsonic server. After following these directions:

First, install Java: sudo apt-get install openjdk-6-jre
Download the Subsonic .deb package and install it: sudo dpkg -i subsonic-x.x.deb

I noticed a dramatic slowdown to the responsiveness of the system over SSH as well as a significantly higher CPU usage. After playing around with subsonic on my phones and tablets I decided the service was not worth the drain on the system. I attempted to uninstall using:

sudo apt-get remove openjdk-6-jre
sudo apt-get remove Subsonic

However after a reboot I still see the same drain on the system, it looks like there are remnants of subsonic, and "top" is reporting a 15% CPU usage by Java when the server is sitting idle.

sudo update-alternatives –config java shows two versions of Java to choose from (6 and 7)

Everything still works, just seems like something is wrong.