Niko, TheSky tells the mount where to go and leaves it to do its thing. StellariumScope, C2A, CdC, HNS all do the same. If it is not winding up where it was told it is because the mount's alignment is not good enough. You might need some more alignment stars to improve the model so the error can be allowed for in the computations. If your mount has a polar align improvement function you could use that, or do a drift align.
By the way, PHD keeps the guide star in the same place in its image. It sends whatever RA and Dec corrections it has to to keep it there but will not stop field rotation caused by misalignment.
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