[Kevin Sevcik]

Mike,
It occurs to me that you've hit the nail on the head. 3 and 4 are opitmized for positions, so they're expecting a quadrature encoder. They look for the B channel on another set of pins (can't remember which) and they will only increment properly if the cycle goes A rise, B rise, A fall, B fall. If B stays high or low, then the code thinks the encoder is fiddling back and forth and not actually turning. There should be a way to fix this in the code, but I don't have it in front of me. That's exactly what the problem is, however.

JG,
Check Kevin's readme and code comments. They should tell you how to use those inputs for velocity instead of position.