With Windows, as you found out, you cannot just move a PCI card for one slot to another without causing some problem with leftover registry entries. Always uninstall the device from thedevice manager first and then move it to another slot.
The easiest, safest, thing to try to get rid of the unwanted registry enteries is to uninstall the card from the device manager, power down and then move the card back to its original slot. Let the drivers reinstall. Then uninstall it from the device manager.
Power down and move it to its current slot.
You could also edit the registry to locate the keys, but, you do so at your own risk.
In the end, I recommned you leave it as is. It does not hurt anything with it being labeled as card 2.