No, probes are compensated fine. What you're seeing above is RC delay components altering the wave shape on NOR gate output, and the other trace is an open-collector output so you're seeing slow rise time due to undriven floating and line capacitance. I wasn't expecting square waves here as my intention was to delay the clock signal enough to capture the "1"s data. The main problem is that the RC delay causes uncertainty in capture edge on the PIC input. So adding another schmitt input gate before the PIC will clean up that edge and allow seeing where the edge occurs and adjusting the RC values to position correctly. I'm working on this right now.