do you maybe build tuxguitar yourselft ?? or download a different release than what are available on downloads section ??
It seems you have "duplicated" classpath entries for plugins.
So you load plugins 2 times. ( See on Tools -> Plugins, i'm sure you have 2 instances of each plugin ).
Take a look to your share/plugins folder. (all files on that folder are dynamically added to classpath).
then take a look to the tuxguitar launcher script.
you have maybe plugins added to classpath too.
> When TG is running there are two "tool tray"/"panel" icons ?
If you see a "tray" icon, is because you have the TuxGuitar-tray plugin installed. that is only an option to miminize tuxguitar to the try ( click on it todo that )
but it's not a new instance of the application.