I think I know what is wrong at least for the vanilla hoppers, they stop when they receive a redstone signal, this behavior can't be prevented, since you put down a lever directly under the machine to force it on, perhaps it sends the signal to the hopper and prevent items from getting in the machine... But that wouldn't explain the buildcraft problem with the pipes, unless a redstone signal also stop them from accepting stuff...
except nothing goes in from a hopper even without the rs signal