Java web start application window size problem in Unity

[Zorrander]

I've been testing out Ubuntu 12.04 and 13.04 for use in our school district. There is one kind of older application that is a Java web start application called A+ Learning Systems that our district uses a lot for credit recovery and other tutorials. The problem I'm running into is that the application is supposed to run in a full screen window (it does this in Gnome, KDE, Windows, etc) but in Unity the window is sized down and does not accomodate the navigation bar. I've attached two pictures in order to demonstrate what I'm talking about. I'm by no means a programmer, nor did I create this application. I'm assuming it is some behavior tied to Unity since all other desktops display correctly. I've searched Google until I'm about to go blind, but have not found any possible solutions. I would really like to use Unity on our student PCs, but this behaviour is going to be a game ender for our really young students. They are like herding cats. :) If any has any ideas, please let me know.

Thanks

http://s1.postimg.org/bp8jkosxr/unity_aplus_window.png (http://s1.postimg.org/bp8jkosxr/unity_aplus_window.png)
http://s1.postimg.org/d5k22tvun/gnome_aplus_window.png