On the long arm, if the seams are open, or aren't laying just to one side, and you are SID, it will cause the SID to jump over a bit at that point.
One thing I've seen is on Sewing with Nancy where she uses lots of steam and then a wood clapper to set those seams nice and flat. I don't have the wood clapper, but it's on my wish list. Also, if you use something like Best Press when you press the block, it seems to get it flatter too.