Hoppers are too 'sensitive' to minecart chests.

When a minecart chest is on top of a hopper by the smallest amount, the hopper picks up the items in the minecart chest. 

In my scenario, when I load the minecart chest with items, the hopper indicated with an arrow (see picture) takes them out immediately before I activate the powered rail. 

To prevent it from happening, I can manually nudge the minecart chest a little bit so it sits completely over the powered rail, and hopper won't collect the items. However, it does defeat the purpose of the automatic smelter.

Thanks.