With an empty stack, the settings the client sends to the game server make it so that you do not get priority during your opponent's postcombat main phase (with the normally correct justification that you can do whatever you were going to do during the end step). The problem comes up only if the last thing your opponent does is get a permanent that has an end-step trigger.
Basically in order to not make this a spaghetti-code one-situation-exception, we need to pretty heavily rework our approach to how the game gives you priority by default. This is a pretty big undertaking.
Also, we're still working on future cardsets, bugfixes, etc. This problem is significant, but it's not the only task vying for our limited attention. #wotc_staff