How do I stop OSX from switching to First-Plan when Javascript popup on Minimized Window appear?

I'm running OSX Mavericks 10.9.5, Firefox 39.7.0.2
What happens is that i'm using an automated script with Selenium for automatic-forms-filling.
Everything is working fine, just like it does on LinuxMint, but the problem is that when i bring another window to first plan (of any program at all) the "minimized" window running the automatic forms gets "maximized" i.e. brought to first plan when a javascript popup appears, thus not enabling me to run that window on background.
Is there a way to run Firefox on OSX in such a way that Windows don't get switched to first plan when PopUps appear? It doesn't seem to have this behavior on LinuxMint.

Hello!
Maybe this links can help you:
https://support.mozilla.org/pt-BR/kb/solucoes-de-problemas-com-plugins-como-flash-java
https://support.mozilla.org/pt-BR/kb/como-desativar-applets-java
This link scan your plug-in's and search for updates:
https://www.mozilla.org/pt-BR/plugincheck/

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