I would like to know the history of the problem - is this new, or has it been a gradual issue? What is the engine make?
This is not my forte, but I would first check (just checks) the setting on your governor controller, the thing for this is see how they are individually set up vis a vis droop. You will need to have identical set up for droop or synchronous setting in order for the machine to share the load equally.
If the boat has been in service for some time, I would suspect these will be fine and require no change. For a little more on this topic see http://www.dieselduck.ca/library/02%20e ... pslab7.htm
So if the controller is fine, I would start looking at the mechanical issue with the engine itself. Start with the simple stuff, fuel and air supplies. When was the last time the fuel filter(s) (primary and secondaries) changed? Is the air filter good - not plugged? Is there plenty of fuel with good positive head, ER fan running? Can the engine maintain a load when on the network by itself. Compare the running parameters between the two engines from the logbook, perhaps something obvious will show up.
If the simple stuff is good, start looking at maintenance on the machine, is it up to date, is the machine hours excessive?
Start looking at the governor, look for mechanical linkage connections are they tight. Some governors have limiting screws that prevent further increases in fuel for demand... if these are not set up properly you may have a physical limitations on the load or response. Some engine - like Cat - have fuel shut off levers that sometimes restrict the fuel when at top end of demand... Governors also don't last forever; how long as it been in service, is the oil supply clean?
These are some things I can think of, I am sure other visitors will have more input.
Hope that helps,