I am using Polou’s 5v optical encoder kit in both a Zumo chassis and in a round robot chassis. In the Zumo, I was able to use a single channel directly to the interrupt pins on my Arduino Uno. This did not work on the round robot. The signal was not big enough. One way to solve this is to use comparators. You get a nice square signal. I then discovered that when you take the encoder wheels off the shafts of the round robot motors, the peak (black) signal was considerably higher than with the encoder wheels present. Putting a black box around the two encoders to simulate the Zomo situation helped a little. Thinking that this lower signal was caused by reflections off the encoder wheels themselves, I painted all wheel surfaces except the one that the encoders use. This improved the signal by one whole volt.
My suggestion is to make the wheels that way. I have attached some photos.
Let me know what you think.