Ed and Fred, thanks, I guess the isolator is the only device between the alternator and the batteries. I'll try probing the voltage when I get a chance (Coach is at the storage facility).
Some other clues are the following:
Chassis Batteries and alternator (rebuilt) are new and this issue was discovered by the guys that rebuilt the alternator. I'd had the alternator rebuilt by Oregon Motorcoach, along with new Chassis batteries replaced, in April last year, then went on a cross country trip. The battery charge rate was in excess of 14.8 (according to Silverleaf). Prior to alternator rebuild, and chassis battery replacement I'd gotten high voltage alarms through the Silverleaf, but don't remember any after replacing and rebuilding charge system, so I thought all was well.
After reaching the east coast and upon my return west, I got to Wisconsin before I saw that suddenly the alternator wasn't charging any longer. I fretted for a holiday weekend to end, so that on Tuesday I could get it looked at, but suddenly it was charging again, so I continued, and got all the way to Yellowstone before getting the warning again from the Silverleaf of undercharging/no charge out of the alternator.
Limped my way through the park using the generator, then stopped in Idaho. That's where the guys told me that "on the bench the rebuilt alternator was giving 14.2V which was spec for the alternator, but as soon as it was placed in the coach, it would give over 15V and they said that sort of thing would fry the alternator and that's probably what happened. They verified that the chassis batteries were fine (up to charge), so that wasn't what was calling for more volts. They weren't familiar with the coach, so what they did was craft an output limiter from the alternator using some sort of electrical wizardry to limit its output to 14.2, and they noted that there was a 1 volt drop to the batteries (13.2 was the max since the alternator was limited to 14.2), but told me by limiting the output of the alternator it would not burn out again. So, I've had this issue since about June of last year, but have been happy with the charge rate which runs from 12.8 to 13.2 on the Silverleaf without causing an alarm condition.
I've read others' postings about having outputs of over 14.2, and I've read all the warnings about running the generator in the morning to pre-charge chassis batteries, but even though that would explain the high demand placed on the alternator, it doesn't explain the voltage drop to the batteries, so I guess I need a new isolator to go back to perfect.
I looked at removing it, but boy that looks like either a lot of work (mainly to get to the bolts) as mine is sandwiched in between two surfaces, or I need specific tools. Anyone done this? I'm not sure if a 2000 year coach has the same setup as mine in the battery compartment as to location of the isolator, but it probably does.
You can see the bottom left corner of the isolator barely visible in this jpeg image -
http://coach.quickreckoning.com/BatteryAndServiceBays.jpg - the bolt visible is the easy one to get to.
Thanks again Ed, and Fred.
Mike