I have never had success trying to sew binding on both sides together. Typically you want to sew it on to one side, then turn the binding and sew the other side. If you want to do both sides by machine, here are my favorite Youtube videos (by Leah Day) on how to do it:
http://www.youtube.com/watch?v=wprg5...7&feature=plpp
http://www.youtube.com/watch?v=7MRfA...eature=related
You don't absolutely have to use a walking foot as she does, but it helps. Starching the binding fabric heavily before cutting the binding strips also helps.