Laptop CD drive problems! cant boot from it

I've got a friends Toshiba Satellite Pro A120, it was running very slow so I said I'd do the usual for him. Backup all his documents then reinstall windows. not so simple!
Firstly, trying to boot from CD so I can boot into Ubuntu or reinstall windows. Took me long enough to work out I had to press DEL/ESC to get into the BIOS, but once I set it to boot from CD (and had a bootable CD in the drive), it just kept booting from the HDD. Every so often I would get an error saying
"Media test failure - check cable"
or something similar, theres lots on the internet about that. I think its something to do with if the boot order has CD first then it has LAN as 2nd.

Managed to boot Ubuntu from pendrive. Trying to copy his documents over to my external drive but was copying really REALLY slow (like 1MB/s) and kept getting I/O errors on a few files. I can't run HDD diagnostic software as I can't boot from CD (could get the Ultimate Boot CD onto a USB stick though if anyone thinks it could help?).

In windows, the CD drive only reads real CDs (like audio and DVDs, not CDRs or DVDRs). does this mean a failing drive? what puzzles me more though, is that I switched the CD drive with a working CD drive from another laptop and windows now doesnt recognise this new CD drive at all! When Putting a bootable CD in this new CD drive it still boots from HDD (not recognising the CD drive at all). The BIOS is a bit useless and doesnt show detected drives....
Also, booting Ubuntu from pendrive, with the original CD drive, it only reads real CDs and DVDs and all copied ones are seen as blank discs, and replacing the CD drive with a known working one in Ubuntu means its not recognised at all (so its not windows driver problems).

When I started messing around with it I do remember windows saying the time had been reset, so I set the time properly, then it did the same again i think. A flat CMOS battery couldnt be responsible for this?

Is the motherboard, and specifically the IDE controller or one of the ports broken, or am I doing something stupid? I'm tempted to just install Ubuntu by USB and tell him not to bother with CDs anymore ;^)

Any suggestions or comments would be much much appreciated!

Thanks,
Dan Gent