There should be just one tube on each of the three slots - is that what you have? The tubes rest on the shaped sides of the slots and block air from the solution which should be pretty much at the level of the tube (ie. zero air space). A lid over the top of the whole processor would not do such a good job.
One tip, label each of the tubes so that you don't put the stop-bath tube on top of the developer by accident . . .