I've always struggled to get good alignment with programs like Alignmaster that require star pairs. With my poor horizons at home it can be a chore to get visible pairs at times too. I expect you'll have trouble if your mount isn't fully orthogonal or if there's any saddle flexure etc, particularly if you have to meridian flip between stars. Obviously not something you want to have, but for those of us with budget mounts we don't have time or expertise to service this can often be the case.
I still have most confidence in drift alignment with a webcam using K3CCDTools as described:
http://www.iceinspace.com.au/63-544-0-0-1-0.html
If you nullify the drift in a scope view you KNOW you've it right. With practice you can get it right in under 30mins at an unfamiliar dark sky site every time - 15mins sometimes. At home I just dump the tripod onto marks on the tiles and away you go with minimal fuss.
