If you have an old reprap.propreties (my old file was from the November 2009 build) and you then run a newer version of the RepRap host software (my newer version was the July 2nd build), then when you go into the Preferences screen on the new software, you won't see new preferences that have been added since the old code. My example was under the extruder tab - I couldn't see the new preference/property Extruder0_ExtrusionPWM.
If you then delete the reprap.properties file from ~/.reprap (or remove ~/.reprap altogether) and rerun the new software, a null pointer exception is thrown, and an empty alert box is displayed (image attached to this bug, and stdout with the exception below). This run DOES create a new reprap.propreties file though, so if you quit and run again, everything works fine, and you have a new updated reprap.properties file that you can modify as you like to incorporate old changes you'd made to your previous version.
stdout when running after deleting the reprap.properties file (this was from the 2010/07/19 build):
Java 3D WARNING : reported GLX version = 1.2
GLX version 1.3 or higher is required
The reported version number may be incorrect. There is a known
ATI driver bug in glXQueryVersion that incorrectly reports the GLX
version as 1.2 when it really is 1.3, so Java 3D will attempt to
Failure trying to initialise extruders in botConsole: java.lang.NullPointerException
Exception in thread "RepRap" java.lang.NullPointerException
at org.reprap.gui.botConsole.XYZTabPanel.initComponents(Unknown Source)
at org.reprap.gui.botConsole.XYZTabPanel.<init>(Unknown Source)
at org.reprap.gui.botConsole.BotConsoleFrame.addExtruderPanels(Unknown Source)
at org.reprap.gui.botConsole.BotConsoleFrame.initComponents(Unknown Source)
at org.reprap.gui.botConsole.BotConsoleFrame.<init>(Unknown Source)
at org.reprap.gui.botConsole.BotConsoleFrame$2.run(Unknown Source)
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