I have an ACER motherboard RS780HVF, which I know is quite old, but Speccy reports the usage of the PCI/PCI express ports incorrectly.
PCI-e x16 is the only one in use, but reports as available.
PCI-e x1 which is empty reports as in use.
1st Standard PCI is empty but reports as in use.
2nd Standard PCI is also empty and correctly reports as available.
Hope this info helps