Joining quests involves special packets. Can the player see the pipe if you place a new one after he joins? Can he see existing pipes when joining freeplay? If both answers are yes, it may just be a quirk with the quest join packet.
We pass the quest join packets raw between the clients, so could just be something glitchy with how BB handles government quests and pipes that already exist when joining.
We can look at this bug, but it's extremely low priority, the other player can use another telepipe or cast Ryuker for you. (Yeah, I know telepipes may be expensive at lower levels, but soon it won't be that bad... trust me. )
Quest joining was a new feature added to BB, so I wouldn't be surprised if it's a bit buggy. Being able to join quests relies solely on the new packet Sega added to BB; previous versions simply can't join quests at all (and even on BB, you can only join certain quests).