fixing this could be as simple as adding in a small pop up that says "you encounter something in the wastes" that works just like if you found something, but it only allows you to enter the encounter, rather than automaticly dropping you in to the encounter.
you just need to make sure the window doesnt go away one you log back in and leaves you stuck on it untill you click "enter encounter", other than that, the only other good side to make up for having to click the damn thing over and over again, is being given a chance to talk tactics with your party if you have one, or heal etc.
-Ulrek-