Do you have EQmod set as "append on sync" or "direct mode". I have to swap between the two because alignmaster needs direct mode but to build a model you have to have it set to "append on sync" if it isnt it wont record any alignment points. The only other reason I can think of is if you have bad backlash in one or both ra and dec.
EQmod will also need quite a few points before accuracy is good across the whole sky, it should however slew to close stars very well after 3-5 points.
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