Maybe Gnome doens’t play nice… I’ve not used Gnome myself in years. When you say you are launching it using the Spark file, are you using the terminal to launch it, or just double-clicking it?
Also, since you mentioned the read/write privs, spark will attempt to make a .Spark file to contain the user account’s preferences and other things in the current users home directory.
I don’t think that’s your problem, just wanted to make sure you knew that too.
Have you verified Spark is actually still running when this happens via TOP or something? It’s possible Spark is not running anymore, and therefore there would not be a tray icon.