Hi "rvn10",
Quadrature encoders do by nature have a phase difference of 90 degrees between channel A and B. This phase difference is required to know in which direction the shaft is rotating when a transition from one of the channels is received. Please see these two links for some useful information:
EncodersLinear and Rotary EncodersQuadrature Encoder / Position MeasurementIf your goal is to measure the angular position using the two quadrature square signals, then your task is quite simple if you use one of our Counter/Timer cards. Check for example the shipping example called "Measure Angular Position.vi".
If you want to read more about our most affordable Counter/Timer product, then check this link:
NI PCI-6601Please let us know if you are using different hardware to acquire the signals.
- Philip Courtois, Thinkbot Solutions