your description doesn't tell us you're real network problems. Also is it not really clear, whether the problems are a result on the attacks on Metro. I guess, letting the Admin team know you're Regions might give them the chance to look onto the server logs?! Not being able to connect to own Regions can of course be caused by a compromised network as well as by a compromised server/pc/...
I, for example had similar problems, when I moved my installation to a new server. Just missed to exchange entries in the regions.ini or somewhere else.
Securing the own environment (and even harder if it is a server) is essential and can be a nightmare. But I guess, visiting http://easyfwgen.morizot.net/gen/
to generate a basic IPTable is a good start. If you are not on a server, you can read out of the iptable config, what should be blocked at you're router and what not. The same, of course applies to the windows (or norton or what ever) firewall.