If you already have code to keep track of the state of your app's UI, you can probably get it to work simply by putting the code in onPause() and onResume(), instead of onStart() and onStop().
It is possible for the UI not to be visible, or partially hidden, even before onStop() gets called ... as you found out.
Take a look at the Android Activity lifecycle diagram here:
http://developer.android.com/images/activity_lifecycle.png
and note the description:
The foreground lifetime of an activity happens between a call to
onResume() until a corresponding call to onPause(). During this time
the activity is in front of all other activities and interacting with
the user. An activity can frequently go between the resumed and paused
states -- for example when the device goes to sleep, when an activity
result is delivered, when a new intent is delivered -- so the code in
these methods should be fairly lightweight.
Read more about this in another question here.