emteria.OS detects the resolution automatically during the boot. If you change the connected screen, the resolution might also change. Depending on the order in which you try which screen, the system may fail to "reset" the old resolution and you will get such strange behavior. If you want to set your resolution yourself, refer to this thread: 
#99
In 0.5.3, we have added a new setting for screen rotation: Settings -> Emteria Settings -> Screen Rotation.
