As described above, this is the procedure I personally use...
When I park, and before I shut off the engine, I use the door lock button on the door to lock all the doors. Then I manually unlock my door by hand. Then I shut off my vehicle. When I exit the vehicle, I manually lock the door by hand and shut it.
This insures the alarm system doesn't arm itself... even by accident. You can verify this by checking your security light. It should be off. When re-entering the vehicle, you're safe to use the key in the door or the remote transmitter to unlock the door. This method should work just fine even if you have glitches in your factory alarm system.
I know it sounds like a pain in the butt... butt it works!