That's hard to diagnose.
A bad power supply could cause both PCIe video cards to come up bad but the MB would report it in the boot beeps.
If the BIOS setting isn't holding for PCIe video, that would explain both PCIe cards not working, and a clear single short boot beep.
As you suggest, if the MB's PCIe slot is bad, though unlikely, both cards would malfunction, but I'd expect the boot beeps to report it.
I learned a long time ago that what a user reports isn't always what's really coming up on his end. That said, going on what you've said, I'd have to go with a missing or bad setting in the BIOS. If you have the manual, start there, if not, download the current manual for your current MB. Look for a setting to enable the PCIe x ## and another one to direct the MB to enable PCIe video. Beyond that, I don't know how I can be more helpful in the forum venue. There might be tech support or an ASUS forum for your board specific board somewhere.