I've heard about this problem a few times in the past but I can't remember a fix! I think somebody was offering replacement boards??
Search on here or try and find a posting on the Dive-In Facebook site, perhaps?
Otherwise John R is your man to repair it.
I don't know this particular board but assuming it uses an H Bridge for motor switching, one or more of the MOSFET transistors has probably popped. (It suggests that the original circuit design was lacking protection for the MOSFETS.)
Again John is your man. He provided advice on this for my proportional piston tank controllers which have now worked perfectly for 5+ years. Neptune are not the only ones with problems in the same area. I was told that Engel also had trouble with H bridges and moved back to relays.
Failing this, if you are reasonably handy with a soldering iron you could try replacing all 4 MOSFETs.
The Neptune seems to be a great sub but has one flaw!