There are some SMT components on the CPU PC board that have to do with PCIe slot one; they are on the opposite corner from the arrow index, at least on x299 CPU's. Can't say for sure on Z370/390. I suggest you might examine the CPU to see if the bottom is perfectly clean, and if there are any missing parts or damage to the PCB, especially the corner area. If you had the MB, I'd say examine that part of the socket to see if there are bent or missing pins.
Have had the same symptom you describe with a x299 CPU. Since I can't repair the PCB, the GPU is in slot two.