Ok the master list issue should be fixed.  

Long story short- GameSpy has this NatNeg protocol that's designed to allow people to run servers behind a NAT.  The machine we run UT3 on has multiple NICs.  One NIC is for the Datacenter's internal network and the other is setup with multiple IPs for public connections.  Well, when I packet sniffed, UT3 wrongly told GameSpy about our internal IP and assumed the query port is blocked behind a NAT.  So that means when you load your server list UT3 tries to ping the server using a different method (ICMP) instead of connecting directly to the query port.  For whatever reason UT3's ICMP implementation uses the old raw socket method which requires elevated permissions.  So, unless you ran UT3 in XP or as administrator you didn't see our server.  I have to temporarily disable the internal NIC to fix this.

Our server isn't the only one affected- there's several servers that are joinable but requires you to run UT3 as an admin to join.  If you run UT3 in XP or have UAC turned off but saw our server as 9999 then that's probably as a result of the server changing the GameSpy ID several times over the past few days.