Skype penetrates firewalls/NAT by fooling stateful detection... could that be what they are referring to?  It also will try to guess at the port that will be used for an outgoing connection by causing an outgoing connection and then portscanning the range above that port in the case of incremental port numbers being used by the firewall/NAT software.

Apparently (according to the article linked in the article you linked) they have changed those behaviors to make them less likely to be fingerprinted.  That could ceertainly make it harder to tell whether it's valid Skype traffic, or whether it's allowable traffic at all, depending if you allow Skype on your network.

I dugg it.  Also submitted a solution.