As of the connection issues earlier in the day, there seems to be potential issues with the daily missions (or at least potentially with the 'do 3 Yearning for Peace' mission).

I was in the middle of my third run when the connection errors hit, and I was booted from the game.

Upon reconnecting after it was back up (and a while longer since I was having lunch after a while) I finished the run, but it didn't show up on my daily mission list.

Doing another 2 runs had neither of them count either, so I rebooted the game, and thankfully that worked to fix it. So if anyone else is having similar problems then try rebooting the game and hopefully that will fix it.