Larry,
When we were in the Sea of Cortez, one time I had a very similar problem. My Link-10 was reading 95%, but my Morningstar (old one) had a red light and I had low voltage when I read it with a meter.
I removed each batter cable connection (at the battery) and cleaned the terminals and connectors. Once I put it all back together, it all started working fine. Sure had me sweating for a time as we were quite a way out at the time.
Good luck!
Greg