Java Based dialer overrides other windows

I work from home on a Java Based program named Five9. While working I am either taking notes for college, or I am playing call of duty in another window. When a call pops up the Java based dialer overrides the window I am working in and Stops whatever I am doing until I click on the window I was working on again. Even as we speak when a call comes in it overrides my keyboard until I re click this window. I am looking for a fix for this and the Dialer tech support refuses to help me. I have literally tried everything I can personally think of and nothing seems to work.

Details,

The dialer is opened through Mozilla firefox
I am running windows 7 64bit Home edition
Computer specs:
AMD Phenom II X6 3.3GHZ
16GB DDR3 1333Mhz Gskill Ripsaw
USB Saitek Keyboard

Using the latest version of Java