Hi Russell,
No such problems in EKOS for me.
Are you using the polar alignment assistant in an Automated fashion? I find it best to do a quick polar alignment with SharpCap and a polemaster type set up. This gets me close. I then use the automated EKOS polar alignment although that is just my routine. As long as you are not miles off EKOS should work on its own. (This won't work if your FOV is too narrow (i.e. SCT F10).
Let it do the 3 captures (push up the speed to X600 as mine wanted to default to X64) and work out the vector. I then go toggle on to the expanded screen and zoom in so that everything is nice and big. Find a bright star and click on it once. The vector path will show up in purple from the star to a cross at the end of the line.
Now toggle back to the polar alignment tab and click refresh (1 sec is OK esp if using the main scope rather than a guidescope). Toggle back to the expanded star field with the alignment vector. Now move your azimuth and alt controls until the star is directly under the cross.
Bingo! you are usually within 5 arc mins of the pole.
Go back to the alignment screen and click done.
The mount will go back to parked position and you are done. You can re-do but I have never found that really worthwhile.
If you want spot on PA you are best to drift align in PhD2 IMHO.
Hope this helps
Mike