I had an incident recently that a skype user connected to a vpn through a Tomato v102 AIO RT-N16 and the skype client/server p2p started using all the ports on the VPN as it's gateway.
This shutdown the site, all packets blocked in and out, except for the skype gatewayvia the pptp 2008 server vpn.
I removed a filter for blocking streaming sites pandora.com grooveshark.com etc.. and the removal of the site filter fixed the problem, skype was happy, all users happy.
So, using skype for many years myself I found this to be the normal virus like way of operation, but it surprised me that a simple site filter could cause issues in the operation of a totally unrelated Skype layer7 and via a unrelated PPTP server on a domain controller, ie port forwarding 1723 to that server.
All I can figure out is Skype could figure it's way in, but not find a way out and used the originating public ip as source, the router iptables rules dropped the rerouted packets as if they were from one of the streaming sites?.
The reason I'm mentioning all this is, If Skype was routed inbound but without a outbound option due to you blocking it's outbound route, you could end up in the same situation.
Probably your best bet is to go into Skype networking and block port 80 and 445 connections, there are check boxes, also assign a port for communications. Using filter rules you can then redirect the port inbound to a null location.
So it communcates out, but not in. The tcp port assigned will switch to a udp port of the same number for voice call streams.