I had same problem on another pool. Then I just say to my self:"Don't fix it if it is not broken and go back on 2.11.4." But never figure out what was wrong... But I'm soon getting ASIC usb keys so I will be forced to go to 3.1.1. So if you can figure it out would be great.
I can't duplicate it locally unfortunately so there will be some restarts as I add debugging to the stratum server and tweak settings.
Edit: Logging lots of debug goodness now.