Just to clarify, there are no other devices present in Device Manager when you are able to see the one FlashPro port? Not necessarily COM ports, but unknown devices, anything that the other ports may have been incorrectly assigned to?
When you reinstalled the drivers did you do it manually or let Windows do it automatically? The drivers should be available in your Libero installation directory for manual installation.
Since you mentioned that uninstalling the driver causes four unknown devices to show up, I think we can rule out the hardware being the problem and that the driver installation process is the issue. It’s not clear to me why exactly you’re losing the other 3 ports though.