The reason this happens, is because DisplayPort is controlled through the driver.
This means that when your OS goes into hibernation/etc, the connection to the monitor is lost. When the computer comes out of this, the connection is restored. Given that your other monitor is not having this issue, all applications are moved to the only active monitor.
There are 2 ways you can overcome this problem
- Make sure all your monitors are driver powered (not sub-d (blue connector) but DVI, hdmi or Display Port.
- Make sure that the 2nd monitor is connected through sub-d and your primary monitor is connected through display port. (this will definitely work)