If Stephan is using his SLT in it's original stock configuration (in Alt Az mode) then polar alignment doesn't enter into the picture.
First I certainly would double check the power source for the mount. Power problems can show up as all sorts of strange and non sensical behaviors. Is this a fairly new SLT scope? What are the firmware levels (from the Version command in the utilities menu)?
Tracking accuracy on a Celestron Alt Az goto mount is dependent on how accurate the initial alignment is. A more accurate initial alignment the better the tracking will be because the mount mimics the RA sidereal motion from simultaneous motions of both the Alt and Az axis'. Those motions vary in different areas of the sky. There can be areas of the sky that a mount doesn't track well in. If you are comparing the goto and tracking accuracy you should be using objects in the same part of the sky. In general, if the goto accuracy is good then the tracking accuracy should be as well.
So first a good initial two star alignment is preferred. Good goto accuracy is the measure of a good initial alignment. As Mlord mentioned using consistent up/right motions for the final centering is important.
Stephan is the tracking (and/or goto accuracy) different between DSO (stars, etc.) compared to solar system objects? If so this is usually because of a problem with local time/location settings. Solar system object positions and motions are calculated from those settings (because they are constantly changing). The static positions of the DSOs are calculated once from the initial alignment. Since CPWI gets it's local time from Windows it is usually very accurate, but location data could be an issue (depending on what location data is used - manually entered or from Windows). I would carefully go through the user data settings (time, date, location, DST setting, and time zone) in CPWI to see if they match those used in your physical hand controller.
Another potential issue affecting tracking is physical backlash. This would however normally also affect the tracking and gotos of all the objects (both DSO and solar system) so I doubt this is your issue. It might however be good to just check this between the physical hand controller and CPWI ... even though the settings for this compensation are supposed to be stored on the motor controller board in the mount and are therefore common no matter which hand controller is used for the initial alignment. https://www.nexstars...ds/Backlash.htm