I have a GTX-960, nothing fancy, but when it runs I get far superior performance than the Intel 4600. I've disabled the IGFX in the Bios, and that seems to have saved. But when I set the graphics to run through PCIE, and save, the next time I enter the bios it is back to "auto". I've been fighting this for months. Sometimes it runs fine, other times it seems to revert to the intel, and gives me serious framerate issues on NBA2k17 at lowest settings. The device manager does not show the Intel graphics, now that it is disabled in the Bios, but somehow it seems to still be running through it? 
 
System Manufacturer EVGA INTERNATIONAL CO.,LTD
BIOS Version/Date American Megatrends Inc. 4.6.5, 3/30/2018
Processor Intel(R) Core(TM) i7-4770 CPU @ 3.40GHz, 3401 Mhz, 4 Core(s), 8 Logical Processor(s)
Installed Physical Memory (RAM) 16.0 GB
Available Physical Memory 11.6 GB
Available Virtual Memory 13.0 GB

That is actually what I had been doing for the last few days, and it's been running well. But I re-enabled it on windows in order to use the hdmi port for a second monitor. And then I tried to fix it in the bios and got really frustrated that it wouldn't save my settings. But I think you are right, I can just keep it disabled in windows. I'm ordering a display port adapter now, so maybe I'm all set.

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That is actually what I had been doing for the last few days, and it's been running well. But I re-enabled it on windows in order to use the hdmi port for a second monitor. And then I tried to fix it in the bios and got really frustrated that it wouldn't save my settings. But I think you are right, I can just keep it disabled in windows. I'm ordering a display port adapter now, so maybe I'm all set.

Do older bios's give you the same issue?