Tried something new today. The problem seems to be with ending your turn with the spacebar during the colosseum matches (the ones you are not asked if you want a rematch).
If I play these matches using spacebar, the game will glitch after the first match is over. From there, no matter what else you do in the game, the glitch "follows you".
If you avoid these matches, the game plays normally.
If I use the mouse for everything during the colosseum matches, the game plays without a hitch (managed to complete the colosseum matches without the bug showing up).
Maybe it is reading more than one key press for some weird reason (pressing resign and then the commoner button)? (not a problem with my keyboard as I tested in 4 different places with the same results)
I also noticed that in IE and firefox I get the flickering, while in chrome I get a new match.
I hadn't noticed this before, because the first thing I do is the colosseum, I always start with the commoners and using the spacebar is a habit already.