Re-boot sounds a bit extreme, if you get another virtual window up (or 'ctrl alt F1' for a terminal), open up a terminal and pgrep java. Then kill the process using kill -s KILL xxxxx (where xxxxx is the offending process id, as sudo if required). From memory there is a bug filed about running linux applications concerning path, ie you can run script from the directory containing the script, but not otherwise. Processing 2.0a5 is more recent version of alpha, failing that you could svn checkout the latest development version. 

2.0a5 is supposed to fix the issue (apparently a bug in the executable script), but I'm getting the same results for the exported application. It asks if I want to run the executable test file, I click"yes", it goes and accesses the drive for a moment or two, and then nothing.

I was going to revert to 1.2 but it's no longer available as an downloadable package.

Any suggestions?

So, turns out my application was halting because it wasn't finding dependencies (specifically a G4P config file). When I sorted that out I was getting a small 100 x 100 aperture in the application. That was because of OpenJava. I had to install Sun Java instead. Now my application works fine in present mode.

That being said, I need the system to boot and launch the application. When I add it to the startup program list for Ubuntu it launches when the system boots but hangs again on a gray fullscreen (like my original issue). It still works as a clickable app, but not as a startup program.

Any ideas why that would be? Is there a way to delay when it launches so that whatever is causing this issue has a chance to catch up (I'm presuming here that tis hanging because something it needs is not yet ready)?

Thanks for all the help.