As I stated before the new azureus (from 4.2.0.8-1) uses java-wrappers for
detecting valid java runtimes (which currently are sun's 5, 6 and openjdk).
There's any issue with this behaviour, because I haven't been reported of any.
Since you're still using 3.* then you may realize that 4.2.0.8-1 is already on
karmic. So I think this is a fix released.
** Changed in: azureus (Ubuntu)
Status: New => Fix Released
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Azureus ignores java alternatives settings and crashes with SIGSEGV
https://bugs.launchpad.net/bugs/199312
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