Alright, I've done some testing and believe I've found the issue. When the phone gets an incoming call, it unlocks itself so you can answer/ignore the call. After the call is answered, the phone automatically re-locks. The mobile shell pops up the now screen when the phone locks, which is why this issue occurs.
I'm experimenting with some code right now which will hopefully fix the issue. I plan to do this by writing a small program that unlocks the phone when a call is answered, and re-locks it at the end of the call.
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