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.