Misbehaving encoders

[nathanww]

Hey guys,
We've been trying to retrofit our Lunacy bot with quadrature encoders so that we can use it for some off-season projects. Unfortunately, the encoders are not cooperating with our plans. Disconnected from the robot, we can apparently read the shift in values from the encoder--but the robot's program doesn't seem capable of reading them(we checked to make sure we were using the right ports, actually starting the encoders, etc)

So, basically what we have is a situation where the robot's digital inputs are not reading the shifts. Our theory is that both the encoder HIGH and the encoder LOW signals are falling on the same side of the HIGH/LOW division when the robot reads it, so it can't pick up the pulse modulation. Does this make sense? Or is there something else that could cause this?