Ian,

When you say "the alternator picks up the -ve from a case connection", do you mean alternator case? If so, there's a small chance that the alternator is isolated. Did you check continuity between the alternator case and the engine block? If none exists, you're good to go.

I had trouble finding an "isolated" 12v alternator when I had to replace mine. The Volvo one I found was not isolated. We ended up modifying it ourselves to isolate it by drilling out the mounting bracket hole to allow for a delrin sleeve around the mounting bolt and also using a delrin washer between the alternator-side bracket and the engine-side bracket.

Then we connected the always-on 12v battery negative to one of the bolts on the alternator case. I have verified with a multimeter that no continuity exists between the alternator and bonding system and that the alternator supplies charging current as intended.

There is, of course, the entire ground isolation solenoid system, which I hope your boat still has.

Note that your masse+/- light is useless in looking for 12v bonding faults as it's designed to look for 24v faults.

At the end of the day, I will roughly quote Olivier when he said that a non-isolated alternator is not ideal, but it's not the end of the world as many other boats have their 12v system connected to bonding. Fix it if you can, but don't panic if you can't right away.

--
Scott 
2007 A54 #69
SV Tengah
http://www.svtengah.com