I then remembered that I had multiple ports on the machine (it's in the attic, I rarely ever see it) and that awhile ago I had activated a second port (if you don't have multiple NICs, it still is the same issue at the network level) and I checked my routes. Bingo. Switched to the other port and instant connection.
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[07:32] <Rabbi_Bob> I'll puke this out so it's in a log somewhere, it may help someone else
[07:33] <Rabbi_Bob> I'm running Ubuntu 12.04LTS on a headless machine (no desktop\gui\etc) and the box has multiple NICs (5).
[07:34] <Rabbi_Bob> If my client machine (172.25.4.100) connects to the first port of the server the following occurs
[07:34] <Rabbi_Bob> Client -> Server: connection handshake
[07:34] <Rabbi_Bob> Client <- Server: ERROR[ServerThread]: Server: peer_id=2: failed to emerge player
[07:35] <Rabbi_Bob> Client -> Server: continues to send information and server receives
[07:35] <Rabbi_Bob> Client -> Server: keeps going, server knows something is there however cannot communicate back
[07:35] <Rabbi_Bob> Server log: ERROR[ServerThread]: Server: peer_id=2: failed to emerge player
[07:36] <Rabbi_Bob> If I move the connection up to another port, it works
[07:36] <Rabbi_Bob> Server: >route -n
[07:36] <Rabbi_Bob> Destination Gateway Genmask Flags Metric Ref Use Iface
[07:36] <Rabbi_Bob> 0.0.0.0 172.25.4.1 0.0.0.0 UG 100 0 0 eth4
[07:36] <Rabbi_Bob> 172.25.4.0 0.0.0.0 255.255.255.0 U 0 0 0 eth4
[07:36] <Rabbi_Bob> 172.25.4.0 0.0.0.0 255.255.255.0 U 0 0 0 eth1
[07:37] <Rabbi_Bob> eth4 is the working nic
[07:37] <Rabbi_Bob> eth1 is the failed to emerge nic
[07:37] <Rabbi_Bob> and it's the route out causing the issue
Does this fix your issue? Probably not and you'll have to figure out how your server is communicating on your network and how things are routing around to fix it. I haven't had time to look beyond getting it to work otherwise and may not bother. I suspect many people will have multiple NICs, especially wireless & wired combinations, and you may need to turn one off while troubleshooting in order to force everything down to one NIC.
For the search engines:
ERROR[ServerThread]: Server: peer_id=2: failed to emerge player
ERROR[ServerThread]: Server: peer_id=3: failed to emerge player
ERROR[ServerThread]: Server: peer_id=6: failed to emerge player