One major factor is that the Software uses both the WPS data as calibration data (Pressure), and the alternator Ripple Signal (for all Cylinders). It then 'tries' to align with the WPS and Alternator data therefore if the alternator Signal is poor, weak or the engine rotational speed is 'erratic' then this can have a huge effect on the way the data is displayed.
Like when doing a manual test, its good practise to make sure the battery is fully charged, the engine cant start, and that the throttle is held wide open. Also make sure the WPS has good battery life i.e. its not about to go flat.
Probably a good idea to save the files if you havent already when using the WPS AND Pico Diagnostics and send them to Pico Technology so they can see the raw data and give as much detail as you can about the vehicle. Alternatively just attach them to this thread and Pico will pick them up here.
For better and more accurate results id advise to use the Standard Compression Test within Pico Diagnostics as this gives pretty good conclusive results and its super quick oppose to taking out every plug (Petrol) or Injector, Glow Plug (Diesel).
There is a video on how to do the 'Relative Compression Test' https://www.picoauto.com/video/relative-compression.html
Alternatively If you want 'Pressure Readings' then id recommend for now using a Manual Gauge, or you could use the WPS500, Alternator Ripple Signal, and do the Test in PicoScope Automotive, this would show you the raw data oppose to nice bar graphs and you would have to do it for every cylinder, which is the benefit of doing it in Pico Diagnostics, you only need to do it in one cylinder.
Then you could reference waveform 3 cylinders and overlay the last one, take measurements and compare on screen but this would take a while to do, so at this point its far easier to do it either with the Manual Guage or just the Standard Compression Test in Pico Diagnostics.
Hopefully this should be more improved in future releases of the Software so keep checking for new releases and check the release notes as this will indicate fixes, features and enhancements.
Hope this helps answer your question