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The blank settings dialog is very peculiar. The dialog should contain a box on the left with just one item "Connection". All of the connection settings should be available on the right. I've never heard of it being completely blank for anyone.
While configuring by hand might be possible, it wouldn't be easy. Settings are stored using a Java preferences mechanism that results in a nasty XML file in Linux. If nothing else works, I'll try to put together a cleaned up settings file that can be edited.
Could you post any console output that comes up when trying to get it configured? Thanks.