The main issue you have here is that BC pipes aren't actually properly inventory aware, and make all of their decisions for each pipe.
This means that if a cobblestone pipe is presented with an item and 2 possible exits (pipes won't send items back the way they came), it sends it randomly down each possible exit. Since one of the 1.3.2 updates (I think), they're now sufficiently aware that, if an exit won't take the item, it'll go down the next route.
The upshot of this is that, if an item can't go into an inventory, it'll go down the next route, but if it can, about half will go into the inventory, and half will go to the other exit.
Iron pipes force items to go in a specific direction, and, if it can't, it'll pop out. It won't let items go through any other route.
Diamond pipes do a restrict and prefer system. If a direction has an item in the filter, then no items other than those will go through that path, BUT, if those items can't go out that way, they'll take another route.
For a little clarification, imagine a straight pipe, with a barrel set to cobblestone underneath, and a stream of items of various types going through. If it pipe over the barrel is stone, then about half the cobblestone will end up in the barrel, and half will continue on. All other items will continue on.
If the pipe is iron, and pointing to the barrel, all of the cobblestone will go into the barrel, and the other items will pop out.
If the pipe is diamond, with cobblestone in the barrel filter, and the other directions empty, then all of the cobble will go into the barrel, and all other items will continue on, including the cobblestone, when the barrel is full.
In contrast, tubes set the routes of the items when they leave the source, so, if there isn't somewhere for the cobble to go, it won't leave the {filter/transposer/sorter/etc}, and, if that inventory becomes invalid en route, the item will go to the next valid inventory. If there are no valid inventories, it'll retrace it's path, and go back into the output of the machine, where it'll sit, blocking the machine, until it has somewhere to go.