The Item Pipes are practically one File of Code if you mean that. So if you know how Inventories work, and skip over all the Utility Functions that deal with actual Slot->Slot Movement of Items, you might understand how the Pipes work.
I looked at the code, but I don’t know much about Minecraft/GT6 internals so I didn’t invest time into it.
I finally turned on that other setup though. It seems like it’s the same sort of issue. It has something to do with item pipe junctions and possibly block filters (junction was after the (blacklist ore dictionary prefix) filter in all cases). I fixed all the instances of the problem by replacing the junction with a hopper. Just now, in the other setup, it didn’t start working after I did that so I replaced the block filter and it started working (as if something had broken the setup last time and this caused some sort of update).
Also, it appears vanilla cobblestone goes through blacklist stone and stoneCobble filters.
Found the Issue why certain stone based prefixes did not work at all, should work now. ^^
I’m guessing the solution was marked after the most recent bumpty-bump, lol.
(Hope so anyway or I have a bug to research!)
I saw how ungol liked my comment, so clearly he noticed that I said i fixed it, so he can mark it as unsolved if it doesn’t work anymore
The Issue was literally “Greg forgot to register his own Rocks to the OreDict”
Wait, so that solved my original problem as well?
I do not know, that is something you need to tell us XD