Never heard of ANYONE putting the key in the door to get it to start!!!!
But if the security system was confused, I could see where that would, maybe, help.

The ONLY thing I would say is that if the battery is over 3 years old, put a new battery in it and see if it clears up after a few of your start-with-two-keys tricks.
These cars can do funny stuff if the battery has a shorted cell, etc.

Anyone else wanna chime in?