The way we pop screens in our app is to explicitly pop the screen you want off the stack, as opposed to just the top-most screen. This either requires keeping track of which screens you have on the stack, or some code to iterate through the screens on the stack and search for the particular screen you want to pop off.
The only way round this I managed to find was what I mentioned in the question. When I want to remove the current screen. I need to check it is the same as the active screen. If it is not the same then I just remove the active screen until I reach the screen I am looking for. This would only happen if a menu or pop up was displayed. Also, I need to add checks to my custom pop-up code to make sure it does not try and remove a screen that has already been removed.
It seems a bit messy but could not find any other alternatives.