Well, after a reboot of my system it seems to be working fine.
Something interesting here is that I remembered was that I cleared by routing tables, then restored them ('route -f', then disable and re-enable LAN adapter). Everything else on my computer worked fine, except minecraft. I realize this is probably not a minecraft bug but probably something in the OS or java, but I'll leave the ticket open just in case anyone wants to investigate.
I had the same thing, although not with command blocks. I found turning the server to peaceful then back fixed the problem.