Hi Jimbob -- If you are looking at a length of uniform transmission line at low frequency, i.e., the length is less than 1/4 wavelength at the highest frequency, then there should be no little squigglies. I would guess that the little squgglies you are reporting are either numercial error or de-embedding error. Unfortunately, all we can do is guess. Sonnet is the only EM company that publishes their full port calibration algorithm as far as I know. (If anyone knows of any others that do full disclosure on this matter, feel free to let us know.) Also, as far as I know, we are the only company with exact de-embedding as well, and we can do that because of our perfectly conducting sidewalls that we use as perfect short circuit reference planes for the port calibration. By "perfect" I mean that the port discontinuity is removed to within numerical precision leaving error due to subsection size as the major source of EM analysis error.
BTW, I just got a report that one of our "competitors" (from my viewpoint, we do not have any 100% competitors) just plain can't figure out why I keep talking about error when everyone else always talks about accuracy!