When I have my monitor (Asus PQ279Q) plugged into the primary display port (B) when booting my resolution is 640x640 (Guessing) until I get to the desktop where it is now 2560 x 1440, when I update my video driver using DDU bios screen and desktop is 640 x 640 (?) until driver is installed then I'm back to 2560 x 1440 again.  Now when I plug my monitor into port (D) closest to the motherboard the bios screen and desktop are always at 2560 x 1440 no matter if it's the Nvidia driver or windows basic graphics driver so is this normal behavior?

I'm not much help, but it sounds like there is a priority display port. At least it gives you the native resolution, when it is done playing around. 

Thanks for the replies!  I checked device manager and for the monitor it was using the windows generic PNP driver (both for port B & D) so I downloaded the monitor driver from Asus and installed but it still has the same behavior as before. Since I am only running a single monitor I will probably just continue to use port D since this gives me native resolution (2560 x 1440) no matter what, would this cause any performance issues?  Thanks again!  
 
My specs if it matters:
I7 7700K @ 4.8ghz
Asus ROG Maximus IX Hero
32 GB DDR4 3200 Corsair Ram
EVGA 1080 TI FE
Samsung 960 Pro 1TB NVMe
Asus PG279Q
 

Yes ports are working, here is the break down:
 
Port B = during boot bios load screen is not native resolution and then at desktop screen is at native resolution using windows PNP driver or Asus driver.
Port D = during boot bios load screen is native resolution and then desktop is also at native resolution using windows PNP or Asus driver.
 
Hope that makes sense, also when you say "reset the monitor" do you mean reset back to default settings? 
I have rebooted the monitor like when changing screen refresh rates in the monitor screen menu (not NV control panel) but that had no affect.

Before starting a legenthy post; if you have any other monitors connected, does disconnecting them fix it? Both port B and D should give you native boot resolution.

Assuming you're not running with CSM enabled (BIOS compatiability mode) then the boot resolution on NVIDIA cards should be the native resolution of your monitor. -- More specifically the boot resolution should be the first detailed timing listed in the monitors EDID chip.

The vBIOS will dump the EDID during startup (before anything is displayed), the UEFI will then load the EFI GOP module from the video cards ROM, the GOP module checks the timings and will try to negotiate a mode switch to the first detailed timing. - Assuming the UEFI supports that timing (resolution) of course.

I've seen some UEFI's that only run in 1024x768, 1080p, some scaled/stretched resolution or even only run in native res using the iGPU. I've also sees some NV GOP modules that are hard limited to 1080p max or won't even display anything on HDMI 2.0 (had a fun conversation with NV techs about the HDMI 2.0 one >_>).

I would try a different port (on the screen itself - each port has its own EDID), update your UEFI, update your vBIOS, update your screens firmware (if available) and make sure the CSM is off. You could also try disabling your iGPU and making sure that monitor is only connected with one cable.

As a last resort you could remove the card, reset your UEFI to defaults and then put the card back in.

Side Notes: Windows display drivers have nothing to do with GOP video modes. That can be the UEFI, the Windows boot animation or whatever. So there's no reason to mess about with display drivers. There is also no reason to install monitor INF's as unless ASUS messed up the EDID (and needs a EDID override) then the PNP monitor driver is perfectly fine.

Poofu1
is the cable in all the way?

Aye, that could be it, happened to me with my regular 1080 of another brand.

Quad5Ny
Before starting a legenthy post; if you have any other monitors connected, does disconnecting them fix it? Both port B and D should give you native boot resolution.

Assuming you're not running with CSM enabled (BIOS compatiability mode) then the boot resolution on NVIDIA cards should be the native resolution of your monitor. -- More specifically the boot resolution should be the first detailed timing listed in the monitors EDID chip.

The vBIOS will dump the EDID during startup (before anything is displayed), the UEFI will then load the EFI GOP module from the video cards ROM, the GOP module checks the timings and will try to negotiate a mode switch to the first detailed timing. - Assuming the UEFI supports that timing (resolution) of course.

I've seen some UEFI's that only run in 1024x768, 1080p, some scaled/stretched resolution or even only run in native res using the iGPU. I've also sees some NV GOP modules that are hard limited to 1080p max or won't even display anything on HDMI 2.0 (had a fun conversation with NV techs about the HDMI 2.0 one >_>).

I would try a different port (on the screen itself - each port has its own EDID), update your UEFI, update your vBIOS, update your screens firmware (if available) and make sure the CSM is off. You could also try disabling your iGPU and making sure that monitor is only connected with one cable.

As a last resort you could remove the card, reset your UEFI to defaults and then put the card back in.

Side Notes: Windows display drivers have nothing to do with GOP video modes. That can be the UEFI, the Windows boot animation or whatever. So there's no reason to mess about with display drivers. There is also no reason to install monitor INF's as unless ASUS messed up the EDID (and needs a EDID override) then the PNP monitor driver is perfectly fine.

Disabling CSM in bios solved my issue and now behaves as posted above by Sajin.  Thanks to everyone for helping out!