Are you sure the problem is not at the footswitch end, either the switch itself or the connection of the tube onto the switch?
I had a problem with air leakage at the connection onto the switch where the tube had hardened. I cured it by cutting off the final inch or so of tube and putting the ‘fresh’ end onto the switch. It solved my problem.
Have you checked the tube connection at the control box end…
Otherwise if the problem really is in the run of tube back to the control box then it is likely to have been damaged at some point maybe where other work has been done in the boat?