Lots of great information in this thread. I had a similar problem and just found a fix for it, so I thought I'd post here for anyone else reading this.
I had a tiled background of a mountain range with a transparent top and I would get an annoying line like you described at the top. I realized that it was actually from the bottom of the mountain range as it tried to loop back around. I put a few transparent pixels at the bottom of the sprite and the line went away!
Thanks everyone!