I disconnect it each time I leave the boat which defeats the purpose.
I would be contacting BSE and confer with technical support....
you can do a bit more trouble shooting by covering half of the solar panel for most of the day and see if the controller still gets as hot...
and...
does it ever change charging modes?
does it shut off at night?
how is the battery(s)?.... are any of them hotter that the others?
if a battery is faulty, the controller may be running wide open to push juice into a battery that has an internal short....
is the controller mounted where air can circulate freely around the back side of it as well?
it shouldnt be completely enclosed and confined, so that air can get in to it and let the heat rise off the back of it...
until you get it resolved, you may be able to blanket the solar panel a bit when you leave the boat so you can still charge the batts, without over amping the panel.... just some ideas....
EDIT... as i was reading your post again, I had another thought.... your 250w panel has a theoretical output of 20amps, your charge controller is an mppt rated for 20watts maximum.... it has been my understanding that a MPPT controller can actually get the maximum output from a panel under the right conditions.... if this is what is happening, then you may be maxing out the limit of the controller..... heat would predictably follow with possible destruction....