I think you're exactly right. Now, why didn't I think of that? .The symptoms and waveforms you posted match exactly to a simple open-collector encoder type where the +rail supplying the pullup resistors is not able to supply enough current and drops the voltage a bit.
This was my thought too, right after Max dumped the sine wave epiphany on me. But (remember, I haven't done any bench testing yet, just conjecture) if I re-read his statement...the wave will only get sine-like at higher RPMs (an encoder with more "lines" will get sine-like at a low RPM than an encoder with less lines)
... I am more inclined to think that it really has nothing to do with speed. You could turn the encoder incredibly slow, 1 rev per day, and still get a sine wave, since the output of the phototransistor is going to be analog, in proportion to the amount of light it recieves. Just like we have dawn and dusk, the phototransistor will experience the same.the field or the light intensity gradually intensifies as the sensor approaches the target or window, reaches a peak and then decreases as the sensor moves out of the window.
...or are you talking about a sine wave coming from the actual output transistors, possibly due to switching time?