If you install Phenote on Linux and then launch it from another directory (without cding to the directory where Phenote is installed), it doesn't know where to find images:
2010-09-14 11:37:22,637 [AWT-EventQueue-0] ERROR util.FileUtil - findUrl: failed to find file images/Save24.gif
2010-09-14 11:37:22,640 [AWT-EventQueue-0] ERROR util.FileUtil - findUrl: failed to find file images/Open24.gif
so it fails to start up.
You can launch Phenote successfully by first cding to the directory where you installed it, but you shouldn't have to do that.