After dealing with it for some time, I got with my networking friend Michael and figured out why the NetConsole output would not show up on my GNU/Linux box (my primary machine). This had the effect of the deploy screen being stuck at "Waiting for cRIO to reboot for the last X seconds forever.
Java’s listening on IPv6 UDP port 6666, the data’s coming in on IPv4 UDP port 6666. The trick is to run java with the “-Djava.net.preferIPv4Stack=true” option. I’m looking into a convenient way to do this.
I hope this helps anyone else who is having the same issue.