Ithemes Security

Couple issues all in one surrounding the Ithemes Security Plugin. I installed it and did a couple of things in the medium list. Then a couple hours akismet and site stats (from jetpack) stopped working and saying my firewall may be causing the issue. Then i figured it was the ithemes security plugin so i undid the changes i made and uninstalled it. After that weird stuff happened. I no longer could connect to plugins to find more plugins. Also i could no longer add files (i used ssh with keys) by using my domain name or outside ip i have to use my internal ip. Does anyone know what happened? Did ithemes touch my firewall settings.