It's tough getting them perfectly straight all the time, especially if the cards aren't perfectly centered in their holders or sleeves.
Are you using the lid open/dark room technique? I found this method much easier as you can see the cards better plus it makes for better looking scans imo.
I have heard CCD scanners are much better as they supposedly just look for the pic/card rather than focus on the holder.
I have tried numerous settings, seen here, but gave up and once I was told out about lid open/dark room technique, I just went with it.
http://www.net54baseball.com/showthread.php?t=224696
This test area is at the bottom of the site and is a great place to practice.
Good luck.