Make sure that your normal storage isn't set to critical. When that is set lower than critical and the assembler does have power it should work, as it just is a normal storage. Also watch out that nothing remains on the input cell. If one resource is full, the rest remains on the input, until it is hauled back to a free storage. Until it is hauled away it will block the input cell.
(I'm not sure if it really needs power while gathering.. Will look when I'm at my computer)