I have the following setup:

chest ( logistical sorter: set dark blue ) -> chest -> hopper ( insert on top )-> basic enriching factory ( input top: output to right side ) -> energized smelter ( input right side: output bottom: transporter config output set to dark green ) -> bin.

I tried with ore and it worked. I tried breaking and placing the factory as well. Not sure what's going on.

Attached screenshots.

Client Logs: logs.zip
Server Logs:
server.zip

Seems to be working now. Sorry.