you rough ppolar alignment is almost surely more error than can be accommodated within eq mod. you should make this more accurate.
if you want to learn drift alignment( and i would highly recommend it) then try this simulator. it taught me how to drift align very quickly with no issues whatsoever. go to this page and then follow the link to the drift alignment simulator. an excellent site.
http://www.petesastrophotography.com/
that said once you know how to do it, alignmaster is fantastic. i tried it for the first time 2 weeks ago and it was an absolute marvel!!
i must iterate it is important to clear the sync and align data in eq mod before doing any star alignments.
good luck. eq mod is a great tool. hope you can get it to work.