I noticed this in my setup as well and I concluded that it was just a display issue.
Due to the setup I was using, I could easily see that although it appeared that the items were bouncing off the tp pipe and going back in the chest, they were in fact not actually returning to the chest. I also made sure that they were arriving at the destination okay, so I wouldnt worry about it unless you notice losing items, or not transferring items correctly. :)