when i use a mod that uses buildcraft and adds its own pipes (like phased teleport pipes or logistic pipes) it can heapen that when items travel through a non-buildcraft pipe and then are put intro a buildcraft pipe the items are not flowing through that pipe but the obove or next to that pipe (depending on orientetion). When the items go intro the next pipe they are rendered correctly

Net sync is a little weird sometimes.

So, is this an issue that needs to be resolved in BC or do I need to continue following the issue at the AP mod site?

If it only happens with Addon pipes, then its probably the Addon's issue.

but the items float next to normal buildcraft pipes i think it is something with passing the item from 1 pipe to another (just speculating though)

Try the Emzuli branch, I fixed a bug with bouncing items that caused them to render heading the wrong direction.

i'll check it out