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check that the subs and top boxes are on the correct amplifiers and are being fed by the right signal. if you are doing our trick and using two matrices for Subs and top boxes you may have the outputs incorrectly wired or swapped on the front.

or a faulty cable or two…

i.e. the fault may not be in the desk will probably be after your frequency dividing device (Desk/X-over/2 wire Speakon for a 4 wire requirement)