I have the same issue and tested it in the latest version of the tekkit 2 modpack (Minecraft 1.12.2). I changed to the logistics pipes version 0.10.4.49 and it still doesnt work. If you need further information, pls tell me

Originally posted by @Celestial0579 in #1649 (comment)

@Celestial0579 have you tested the behavior of the extractor module by replacing the stone macerator with a vanilla chest? I can confirm that the stone macerator and the extractor module currently do not work, but I do not believe it is a general extractor module fault.

Seems like it works good with vanilla inventorys. I placed a hopper below the stone macerator and below the hopper i placed a chest. The extraction module now extracts from the chest.

The Iron furnace is now replaced with a vanilla furnace and it work good for this part too. hope the infos are helpfull.