I don't like coming to help for PC issues but I don't even know how to diagnose it. I should have posted this after it initially happened but I didn't.

After a system crash (which happened not under my supervision) one of my 2 on board ethernet adapters was missing from network connections. It was the gigabit adapter. Not only was it missing from network connections but it wasn't recognized by the system and it was non functioning... Ok I figure my mother is now a few years old and maybe it just bit the dust. So in the meantime I just throw an extra PCI network adapter in. The new card serves my XBox via crossover cable. The regular 10/100 on board adapter connects to my switch.

Just a week or so ago I did a format, re-installed windows (also I got a dual-boot with Ubuntu 7.1) after setup, to my surprise. My gigabit adapter was back! However, now the 10/100 on board adapter is missing.. so wtf? It's not working like the gigabit adapter was after the crash.

Ubuntu doesn't even recognize the onboard 10/100 adapter.

And another thing.. When I turn my Xbox on and connect to XBL, my PC still says that the network cable is unplugged. Even though it is obviously working.

Any input would be appreciated.

I don't have the solution but I would recommend seeing which IRQ its being assigned and if possible in the bios force it to use another IRQ. Does disabling the onboard NIC cause the PCI NIC to be recognised?

I have a similar problem in an older computer. Every so often after a reboot the sound card will not get recognised. The 'temp' solution has been to take the card out of the slot and reinsert. I would think the standard HARD reset would do the same thing but it seems to require the actaul act of removing it. My guess is the card is going bad, since it seems to happen no matter which PCI slot it occupies.

Nope

I dunno if it makes a difference but it's a MSI/nForce board

I didn't see any mention of the PCI NIC after you reinstalled Windows. Do you still have the PCI NIC installed? If so is it still functioning in both Windows as well as Ubuntu?

If you do have the PCI card installed, which Local Area Connection in Network Connections is giving you the "Network Cable Unplugged" error, it should show you the name when you see the balloon notification, but if not move the moues over the connection icon in the system tray to find out.

Does the gigabit controller seem to be functioning properly?

Anything else on the motherboard seem to be failing, USB ports, PS/2 Ports, serial ports, vga ports, sound ports etc...

If you have a cable plugged into the on-board 10/100 NIC that's not functioning, do you even get any NIC Lights? (As impossible as it might seem)

Does the Windows Device Manager show any unknown devices?

Finally, do you have a manual for your motherboard that you could check through to see if it is possible that there are any jumpers on the motherboard that could be used to disable any of the NICs and if so, if you check the/those jumper(s) are they securely in the position they should be to allow the NICs to function?

Yes, after the installation of windows the PCI NIC was still installed and functioning in both OS's. The gigabit controller is working. All other ports are working. And yes the light does come on when something is plugged into it. No unknown devices in device manager. I checked the motherboard manual, couldn't find any jumpers to enable/disable NIC

Starting to sound software/firmware could be the issue.

Have you checked your BIOS to ensure there are no settings in there that disables the NIC. Far too often I have seen some BIOS settings reset.

If yes, then after you reinstalled Windows, did you use the CD your motherboard came with and reinstall all the software and drivers (excluding any trial software, and of course assuming your motherboard came with a CD)?

yes I did use the mobo CD to install all the software and drivers necessary. I haven't checked BIOS yet but I always run the failsafe-defaults