Same with me. However, I don't think I was correct about the gold pipes fixing the problem. Upon further testing, I found out they were working all along. The item appears to not go through the teleport pipe, but in fact does make it to its final destination (even though you can still see it stuck bouncing off the pipe). Try it out and let me know if it is the same for you.
For example, in my server, I have a section where both ends of a pipe system are teleport pipes. When the items come out of one (and is then supposed to go through the other) it just keeps bouncing off of the other one. The items are then stuck perpetually inside the system. However, when I looked at the supposed destination, the items do end up where they are supposed to go, even though they still appear to be stuck in the pipes. This was all before clicking the GUI on any pipe upon a server reload. The outgoing pipe said it was connected to 0 pipes, yet it still works.
So, there is still a glitch because you get a large build up of items that appear stuck in pipes (like in my system), but the teleport pipes still do their job.