WhiteWolf So many PCI-e riser cables are not capable of carrying the full PCI-e 4 bandwidth. However, PCI-e risers are transparent to the motherboard, the motherboard doesn't know that the riser exists as there's no chip or communication built into the riser to tell the motherboard this. So the mobo just sees that the GPU suppports PCI-e 4, and that the slot that the GPU is plugged into supports PCI-e 4 and so sets the connection to PCI-e 4. This causes issues if the cable cannot handle the greater transmit speeds of that, which is solved by setting the connection to PCI-e 3 as you discovered.
You can also get PCI-e 4 risers that support the full spec. Whether or not this is worth it in your case is debatable, limiting a 3060 to PCI-e 3 likely reduces performance by only a few percent as it's not really bandwidth starved generally.