Needing to use engine alternator vs. generator

I have never been "at anchor" longer than a week or two, but am now in the Caribbean where anchoring for a long is the norm. As a result I have not had a "full charge" on my batteries in 6 weeks. This is causing some confusion with the battery monitor and the charging systems.

I am finding that the engines alternator puts in a lot more amps than the generator - more or less double the amps. I hate to run the engine at anchor, I don't need the extra hours of running at idle, but with the generator the amps going in gets to be 20 amps or below quickly and I can be getting 40 or 50 at the same time with the alternator from the engine. They alternator has a separate regulator. Here's the setup:

* 90-100, 135 Amp Balamar alternator on Yanmar 4jh - regulated by a separate Xantrex XAR digital alternator regulator (a multistage regulator).

* Westerbeke 6KW generator, regulated by running through a Xantrex a Freedom 20 charger/inverter/(with a multi stage regulator)

My question is this.... Shouldn't a 6kw generator be able to put in as many or more amps than an engine alternator to charge the batteries? I believe somehow the Xantrex Freedom 20 inverter is "throttling down" the amps from the generator to a lower acceptance level than the separate, free standing alternator that the engine alternator uses. I know I want multi stage charging, but why would the Freedom 20 throttle it down to such a low level? I would much rather run my generator for the same amount of time.

As far as I know there is no way to change the allowed charging rate on the Freedom 20 regulator.

So here I am, in a harbor with a perfectly good generator, charging my batteries using the boats engine. That doesn't seem right.

Any ideas?