I was about to report something similar with inputting items actually, so I'll leave a little reproduction, expectation and reality thing you can go back and edit in (Mojira mods feel free to refer to this):
Reproduction: Set up a redstone clock hooked to a crafter (I put mine on orientation: east_up). Have a rail with one or more hopper minecarts on top of the crafter. Put a chest in front of the crafter and above the hopper minecarts, and fill the hopper minecarts with... let's say gold nuggets because that's what I used to test.
Expectation: The hopper minecart(s) would be able to input items into the crafter just like a hopper would, and craft the golden nuggets into golden bars at a fast rate.
Reality: The crafter remains empty, the hopper minecarts do not get emptied out, thus the golden nuggets remain inside the hopper minecart(s).
YCSAWAMPFP
I was about to report something similar with inputting items actually, so I'll leave a little reproduction, expectation and reality thing you can go back and edit in (Mojira mods feel free to refer to this):
Reproduction: Set up a redstone clock hooked to a crafter (I put mine on orientation: east_up). Have a rail with one or more hopper minecarts on top of the crafter. Put a chest in front of the crafter and above the hopper minecarts, and fill the hopper minecarts with... let's say gold nuggets because that's what I used to test.
Expectation: The hopper minecart(s) would be able to input items into the crafter just like a hopper would, and craft the golden nuggets into golden bars at a fast rate.
Reality: The crafter remains empty, the hopper minecarts do not get emptied out, thus the golden nuggets remain inside the hopper minecart(s).