Let me see if I understand you correctly.
You have a batch washer (looks like a dishwasher).
There is a top and bottom spray fixture, which would normally spray water up at the board and down at the board being washed.
When you place boards in the chamber, water is only being sprayed from the top spray fixture.
Does that about sum it up?
If so, in general, there is one pump that pushes water to all of the spray fixtures; so, if you're getting water out of the top, it's pretty likely that the pump is working fine. Start off by removing the spraying fixture, and cleaning it out, including all of the nozzles in the fixture (it's great if the nozzles are removeable). While the fixture is off, ensure that the supply line to the fixture is not blocked. Foreign objects, parts, component leads, old solder, etc, can get into the spray nozzles, and prevent water from flowing. The same objects could end up in the supply line, as well.
Cheers, ..rob
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