setup was unable to automatically close all applications

I recently made a change in our application (Application.Run(ApplicationContext) instead of Application.Run(Form)) and ever since I made that change, the ISLE installer fails to close the running application in order to install a later version of the application.

When the ISLE installer tries to close the running application, how exactly does it signal the running application to close?

I'd like to figure out what signal or method or event I need to handle, in order to make the application close successfully.

Thanks...