WTF was that? PC goes haywire after Java update.

So I got the latest Java update. As always Firefox froze for a minute.

I went on until I wanted to start jDownloader (a Java app) but I got an error saying the .jar file was corrupted or incompatible. At the same time I finished the update the external sound card started to stutter.

Well, time for a reboot I thought. I do so and on reboot I get an error saying "disk read error press Ctrl+Alt+Del to reboot"

I rebooted with the install disc, same error. Same with the system recovery disc.

I set bios setup to default and boot a Linux CD (Partition Magic). Surprisingly it boots but can't recognize the boot disc (io error), the other ones seem to be okay. At this time the keyboard needs to be unplugged and plugged again after the OS started to be recognized at all. This never happened before.

I guessed the boot disc was dead and since there was nothing else to do until Monday I popped in the install disc again and lo and behold it booted directly into my running system.

Now I'm afraid what'll happen when I shut it down for the night.

Any thoughts?

Edit: Two reboots later everything seems back to normal. Still clueless what happened.