I was going to plant the banner while playing as Oak when a desync box comes up, which was annoyingly coming up for a while, only this time my mouse disappeared and I couldn't click it. The box also over rode hot key commands and the options screen so I was just stuck for the rest of the game.
[UPDATE]
It would let me move the camera with the directional buttons and asdw. I was also able to get my mouse back by hitting alt + f4 and saying no.