This is the second time I've seen someone in #ubuntu do this.
When you install sun-java6-jre, it will instruct you to go download something and drop it in /tmp and hit enter (something like that). For some reason I do not understand, some users just hit enter without downloading the file they were supposed to and putting it where they were supposed to. Of course, computers don't like it when users don't follow directions. The result is that apt sits there waiting…and waiting…and waiting. Eventually the user assumes everything is done and shuts down. Or maybe they try to install something else and find the dpkg lock in place and try to forcibly kill it or force shut down. Since Java is half-configured, dpkg ends up in an inconsistent state that lasts across reboots and is a pain to try to sort out.
All because somebody can't follow directions.
EDIT: So someone's said in comments that you only get prompted if you install on the command line. Synaptic just hangs waiting for an answer to a question it hasn't even asked. Yikes!