Looks like the Ubuntu (jaunty amd64) build of Java 6 (1.6.0_13) has a problem closing files. Upgrading to 1.6.0_14 from karmic backports Works For Me.
Seems like it would be a big obvious bug, but I couldn’t find any reports. Have you run across it?
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Joe Halliwell's Blog 
Can’t.. resist.. the lure..
How about getting a Mac instead?
http://www.google.co.uk/search?hl=en&safe=off&q=mac+java+problems&btnG=Search&meta=