If an item that was sucked in by a pipe has to choose its direction randomly, the render may go in a different direction than the item.
In addition, when an item hits a pipe-end in a certain way, the item will be sucked up by the pipe but will not render within it.

Relevant mod versions:
forge-14.23.5.2338
AutoRegLib-1.3-29
Quark-r1.5-152

part 2 was fixed in dev. Part 1... hrm. I'll see how I can deal with that.

Actually, the fix for part 2 solved part 1 as well.