Dear Raman,
Multiple popups of Java console can occur if you have one/more iframe or servlet embedded in your page.
In Java control Panel, "Hide Java console" option alone may not be sufficient stop these popups.
Before applying the changes, I hope you have unchecked all the Debugging related check-boxes (Tracing, Logging & Life-cycle Exceptions) which also cause the Console to popup.
Then a restart of your browser if not PC should stop these popups.
I am using JRE1.7.45 on IE9,10&11, haven't faced this issue while switching on/off the console. If the popups repeat, you may downgrade your JRE as required.
With regards,
Ponilango P
