Hi, I've managed to test this a bit more now. Shining an LED at the CCD the red channel never goes above 255 on the scanner sensitivity screen while the green and blue go from around 1500 to about 4995 which seems to be the maximum. So the it seems that the CCD or something after that is causing the problem.
I also switched the two flat cables at the back--p31 and p30-- to see what happens and the green and blue channel showed around 200 whilst the IR channel went up to about 2000. The red stayed at nothing. (I also completely swapped the cables to make sure they weren't damaged and it shows the same results so cables seems fine.)
So I'm thinking the CCD is struggling or the circuits on the CCD or the scanner control PCB. RED isnt getting amplified. It does go up to 255 from around 100 if I shine a strong red light at the CCD.
I'll be very grateful for any ideas on this one!