Just out of curiosity I have just opened an instance of the IDE (1.5.6) with the blank program in it and set the board to Mega and the port to ttyS0 (I have no Arduinos connected).
Then I opened a second instance and set the board to Uno and the port to ttyS1. When I switch from one instance to the other they each retain their settings.
And just to be clear (because this is what may be causing confusion) I started two completely separate instances of the IDE from the operating system. I did NOT create a second "window" from the first instance.
...R