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Being within 3 or 4 arc mins of polar alignment is probably the best you will practically do with the simpler GEM's. There are many factors that will influence getting any closer than that. The most significant in your case is probably flexure in the system depending on the attitude of the "load". A "perfect" polar alignment done by drift alignment on a star moving a few degrees either side of the meridian will not necessarily be the same as one done totally one side or the other even if you have perfectly balanced the system.
A mount like the G11 has the polar axis supported between two bearings that are only about 9" apart. Even with the bearings as tight as possible there will be some give with a heavy load.
Other factors like orthogonality may also be having a bearing when you get down the the 2 or 3 arc minute errors.
The error readings given by various software programs are usually based on positions of stars after alignment and depending on where the stars are will affect flexing and refraction so you could easily be "chasing your tail"
Barry
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