I have activity A->B in the stack, and to launch activity C, I call
Intent starter = new Intent(context, MainActivity.class);
starter.setFlags(Intent.FLAG_ACTIVITY_NEW_TASK | Intent.FLAG_ACTIVITY_CLEAR_TOP);
context.startActivity(starter);
This all works fine, Activity A and B both have OnDestroy called. If I press the hardware 'back' button now, the activity appropriately finishes and is hidden. The problem is now however, if I return to the application through the application by clicking the hardware recent apps button, it will return to Activity A. Activity was destroyed and not in the stack. In the manifest, none of activities have had a android:launchMode set, so they are on default.
The only other possible piece of relevant information is that there is an Activity X that is a launcher Activity that is android:launchMode="singleInstance" and it launches activity A, that being said, it gets destroyed and it shouldn't be in that activity stack anyways.