Well this was timely. I just replaced the controller in my solar panel setup, which is similar to yours. I had an old flexcharge controller and the system was never able to fully charge my batteries. While kicking around the web I came across one of Maine Sail's latest tutorial type posts on his website, relating to solar panel installations. It can be found here: Installing A Small Marine Solar System Photo Gallery by Compass Marine at pbase.com
I have a LinkLite monitor installed, so I can see relatively accurately what is going on with my batteries. Since installing the new controller (I went with a Genasun) it is like night and day. Before, my 300 amp bank was always at least 30 amps short of being fully charged. Last night, it was 0.5 amps short.
So I can't answer your question about whether the marine ones are different, but I can tell you that going with an MPPT type controller made a huge difference. The Genasun ones weren't that expensive either.
Maine Sail: Thanks again for sharing. The amount of excellent information you have made available has been just tremendous.