Hi Jay,
The Application.form file is a file descriptor that describe how the UI looks like, based on Swing. If you update teh Application.java class without updating the Application.form file you will start having troubles. The .form files are automatically updated by IDE such as Netbeans which uses something called Mattise to generate those .form files.
I recommed you to create your own UI using a technology that you know how to use, and just copy the logic from the Application.java class which is related with the interactions with the jBPM5 framework.
Cheers