So I fussed with it for a while. Got sidetracked. Learned a few things. First, open crates won't pass items into an item grate without an air block between. Fixed that.
Second, there are dupe bugs with the Transvector Interface. I'm using one to hopper the goods into an open crate above the furnace to make the most of the cramped space I put it in, and now I'm occasionally getting more glass than I put in sand, more stone than I put in cobble. More ingots than double the clusters I put in (they are working for me). I can't match the problem you're describing, though. Can you give some screens of your arrangement?
Specifically, 33 gold clusters turned into 126 ingots. I'm not complaining, but it's almost as messed up in the other direction as what you're getting.