It probably try to use the GPU you just hide from dom0.
Assuming you used the correct value for rd.qubes.hide_pci:
- Only plug your primary GPU to your primary screen.
- Once you successfully booted into Qubes, plug the secondary GPU to the secondary screen
Also did you checked my comment about this subject
Note: if after this step when you reboot the computer you get stuck in the QubesOS startup that means you are trying to use the GPU you just hide. Check your BIOS options. Also check the cables, BIOS have some GPU priority based on the type of cable. For example, DisplayPort can be favoured over HDMI.