Keith I think your original guess was correct and that the motherboard maybe at fault as you have eliminated other items by swapping them out.
I may suggest you check all the pins are present on the motherboard side, but other than that you're stuck with either a new motherboard or a USB CD drive.
On the brightside, if you swap the motherboard like-for-like then you shouldn't need to reinstall. The model number and make will be printed on the motherboard somewhere.
You could also try clearing the bios as it maybe disabled somewhere in there or maybe the settings are corrupt but that shouldn't affect windows as it doesn't use the bios system to access hardware.
Load factory settings or similar should do it, or to be thorough try pulling the power cable out and removing the button battery (there's also a jumper, normally #12 or 14 which is the same as pulling the battery)
EDIT: it may also be the PSU - power issues can cause all sorts of random errors, try unplugging the HDD or other items.
You could also try plugging the CD into the IDE port that the HDD normally uses to see if it works there, if it does then you know it's just the second IDE port.
Last edited by moozaad : 17-Jun-2009 at 11:22 PM.