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?
There are, it seems, crashers in recent Ubuntu 8.10 amd64 sun-java6-jre packages. Eclipse seems especially adept at finding them. Here’s the fix that worked for us. Add the following to your $ECLIPSE_INSTALL/eclipse.ini:
And some background: