Thank you all for your input. It seems this was never going to be as easy as i initially thought.

I have not had much chance to play with the setup just yet. I have been concentrating on trying to print better disks. If the toner is totally opaque, it will block IR.

Alain you may use this method for UV exposure of your boards but UV is at the other end of the spectrum to IR. We can't really expect them to perform the same.

I have a 10k resistor on the collector of the transistor now, and as i have stated before, this setup works perfectly with other objects breaking the beam. No silly mass counts or bouncing of the circuit. The only other thing i thought of (and what nick just mentioned) was to reduce the intensity of the IR LED to see if it is less likely to penetrate any flaws in the toner (at least limit it enough to keep the transistor off).

Failing that, Although super awkward for something this small, i'll probably have a shot at aligning 2 disks as Al mentioned earlier.

I'm almost there - I don't really want to go to a full re-design of the sensors just yet...