I think this thread has grown in scope. I did use Halscope to look at the signals as suggested by Chris Radek and it showed a discontinuity in the encoder velocity. This led me to looking at the regularity of the index pulse which was found to be flawed. I didn't take any pictures of the Halscope measurements so I assume the post you saw was from another user's problem. In any case, I can't expect the tapping cycle to be reliable if the signals from my encoder are not being accurately relayed to the computer. I'll focus on getting that right before I look any further into LinuxCNC configuration.
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