I agree with Lyra's comment.
A useful check if your batteries are of the type where you have access to each cell is to check the density of the electrolyte within each cell. Using a hydrometer, the density of the liquid should be 1.250, but might be anywhere between 1.200 and 1.300. What you are looking for is whether there are any cells where the density is particularly low, and also if there are any cells where the electrolyte is below the top of the plates. A cell with very low density would point to a dud battery, one that needs to be changed. Very low electrolyte levels would also point to a battery that is not holding its charge and which in consequence will be giving off a lot of hydrogen gas resulting in depletion of the electrolyte. Take care when checking the electrolyte as this stuff contains a mixture of de-ionised water (harmless) and sulphuric acid (very dangerous). The acid will burn a hole in your clothing and your skin and you particularly need to wear eye protection as the liquid within the cells will bubble while charging is in progress, and spitting tiny droplets in all directions as each bubble bursts. Low electrolyte levels can be topped up using de-ionised water to a point where all of the plates within each cell are covered.
My guess is that your batteries are most likely knackered, but in your description you mentioned turning off the red isolation switch. Why you would want to do that I don't know, but normally with an engine running that switch should be on, and not turned off at least until after your engine has been stopped. I'm not sure if turning it off with the engine running is likely to damage your alternator, but I would not want to take that risk.
Normally turning the red switch on, is one of the first things I do when going onboard my boat, it remains on throughout the time I am onboard, and is one of the last things I turn off prior to leaving.
Good luck with your investigations.
