I'm guessing you also have two alternators and so each battery is directly wired to it's own alternator and possibly voltage regulator without passing through the switch. Running on "Both" would have the regulators "seeing" each other and, if there are seperate voltage regulators, thinking the system didn't need full charge and dropping out. (What he said above).
You need a seperate starting battery for each engine and a house bank to carry the loads when the motors aren't running . . . if that ever happens on one if those boats. ;-)
Charlie P. Mud Hen 17 #69 Mad Hatter
To travel hopefully is a better thing than to arrive - R.L. Stevenson
I suspect that, if you should go to the end of the world, you would find somebody there going farther . . . - H.D. Thoreau