We have been having a few issues with teleport pipes recently. A couple weeks ago a pipe placed by Killmeded corrupted a chunk for some reason. Every time the server loaded this chunk it crashed the server. Fortunately the chunk it question was not loaded by an anchor, so I was able to login and roll back his recent changes to correct the issue. We are not going to always be that lucky, and may at times have to restore from a backup.
Recently the teleport pipes stopped working in our new world. In the reading that I have done the pipes at times do not work on multiworld setups. They will work on some worlds an not others. Seems they will work on each of the worlds individually if that world is the only world the server manages, but with multiple worlds they will randomly not work on some of them.
Previously they were working on the new world, even though we had the old world loaded as well. I just recently added another world to the server, which is probably what triggered the pipes to stop working on the new world, although they still work on the new world's nether. I was going to be adding another 2 worlds this weekend, which may fix break the pipes on these different worlds again.
I have yet to find the triggers that cause them to work in one world and not on another, and I may not be able to find one. The reason is many of the Tekkit servers out there disable the teleport pipes, due to the risk of corrupting chunks. They are generally considered more trouble than they are worth. After the event with Killmeded stated above, I did consider disabling them as well. I would prefer not to as the pipes are very useful.
I'm going to look into it a little further to see if there is a way around the issue of chunk corruption and multiworld support, but if I cannot find solutions, we may need to disable them.