msp430FR6989 board code problem
The issue is that your last if statement is lacking braces, so only that first statement of P1OUT &amp;= ~redLED is happening with that if statement. This means that the P9OUT &amp;= ~greenLED; is happening at the end of every loop iteration. 

From your code I would expect whichever switch to be activated first to turn on the LED, the if it is the green LED, it will turn off at the end of the loop so it should flicker at probably at a couple clock cycles of your controller.

If it is the Red LED, it should stay on until both buttons are pressed, releasing the button should leave the Red LED on.

A second button press, simultaneous to the first, will shut off only the Red LED, but the green LED will shutoff every loop regardless since it is outside of the if statement.