Oh been there done that. After a lot time in front of the scope I found the following issues when creating my own optical wheels.
1). photo transistor collector resistor if set too high will bounce output pulses. IE, it is too sensitive to ambient light. I suggest you take a black pen cap and poke a hole in the end facing the LED. This is just for a test to dial in the problem. Also try 4.7K~30K collector resistor using a 5v supply to stiffen the response to eliminate bounce. Try to change LED output level too. You will find through paper the difference between thresholds is very narrow, see point number 2 below if that is the case.
2). IR goes through paper even printed with black ink. The best optical wheel is one made of 0.020 black plastic or better yet aluminum with windows for stripes.
3). Try edge reflection rather than break beam. The problem will be how thin the stripes are on the disk. The finer you go the more likely you need surface mount parts with reduced photo transistor sensing area and narrower LED output. You will need a pin point light source/detector. I made quite a few with surface mount, the challenge is alignment affix all optics to the same board and space correctly.
Nick
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