North poles only attract south poles and vice versa. Stir bars tend to be north on one end and south on the other, even when they are build of two magnets. If you use 2 magnets on your stir plate, you have to make one north pole up and one south pole up or both sides of the plate will be trying...
Your problem sounds like you aren't matching the poles to the stir bar.
This article explains it pretty well.
http://www.kjmagnetics.com/blog.asp?p=stir-bars