Hello Lee,
You are probably using Windows 10 Anniversary Update onwards.
This is the current expected OS behaviour when both graphics card exists, the operating system will use the graphic card used for POST (boot, BIOS).
Should your platform allows disabling the onboard graphics totally, then this would work.
Otherwise, there is an OS improvement scheduled to address this in a future Windows 10 version so the indirect displays can suggest which card to use (=the best one, not the first one).
There is nothing you can change when the OS has booted to alter behaviour.
Kind regards,
Alban
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