The BIOS setting wouldn't change by installing Windows, so it must have been disabled. Because you said the only connection you can get is 1394 (firewire), I assumed you meant you really could only use the firewire connection (ie no USB connection)? This is why I thought it was at a higher level than the BIOS.
If you notice this setting switching off on you in the future, it could indicate an issue with the LAN controller on the motherboard or an issue with the motherboard in general.
Glad you got it working though.