Hi Duncan,
whats your pulse guide rate on EQMOD interface?
The pulseguide speed rate can be set between x0.1 to x0.9 of the sidereal rate at increments of 0.1 independently on each motor (RA or Dec).
At times i get into similar problem even when my alignment is quite spot on.
There are few posts which suggest you to set them to .9x rather than default .1x. I am new to guiding as well so cant say for sure but from my personal experience .1x takes very long to calibrate and sometime gives me trail. I usually set my rate to .7x - .9x region.
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