Cockpit Ammeter
Stephen, you really need to do two things. Get rid of your cockpit ammeter and replace it with a voltmeter. (You could also get a cockpit ammeter with a remote shunt and only run the shunt wiring to the ammeter.)
The reason? ALL of your charging is running from the alternator output (AO) all the way to the cockpit and then back to your batteries. This is usually done in relatively small wire, with large voltage drop.
We have been discussing this "design" for many years here on this and other forums. That design was workable back when there weren't many electrical loads on boats. It's at least 30 years old. The age of your boat, unless modified by a PO or by you, is a dead giveaway that you have this old system.
Think about it: you want to have all the current going from the AO to your house bank as cleanly and quickly as possible.
For some reading, try the "explanation" that Catalina/Seaward provided in the early 90's about why their "enhanced" engine panel was necessary:
http://www.c34.org/wiki/index.php?title=Engine_Harness_Upgrade
While it relates to the Catalina wiring harness issue (bad connectors) it's really the BASIC DESIGN FLAW of cockpit ammeters.
Also check out my article on Ammeters & Shunts 101 which is linked at the top of that article.
I have an ammeter in my boat (in addition to my Link 2000), it is located on the positive side of the system, down at the nav station. It is on the positive wire between the 1-2-B switch and the DC distribution panel. Anything that goes "On" passes through the ammeter and shows up. Simple. It's completely OUT of the AO charging circuit. Where it belongs.