Hi Paul,
a 200km/s error with the ALPY does seem unexpectedly large (roughly a pixel or so). Like you I find the ALPY very stable and I would expect to be able to measure the position of a strong narrow line in an extended object like a PN to better than say 1/5 pixel. In stellar RV work one source of significant error is the position of the target on the slit. (if the star is too small it “rattles” in the slit and even if overspilling the slit, slight offsets in guide position alter the shape of the line profile and move the centroid.) I would not expect these issues with PN though as they are effectively extended objects. Since the error is variable we can also rule out an offset in the calibration lamp spectrum. PN are expanding so show different RV depending on the area examined but I understand these are only a few tens of km/s at most.
I dont know the quality of the wavelength measurement on Plotspectra. Have you tried measuring the lines in ISIS? Also since the ALPY calibration is so stable and you are comparing the PN using lines at the same wavelength, you could try just overlaying the raw uncalibrated profiles of the two PN and look for any shift directly to eliminate any potential errors in wavelength calibration.
Cheers
Robin