Join Date: Aug 2006
Location: Arlington, VA
Thanked 14 Times in 12 Posts
Rep Power: 12
My recommendation is that you consult a knowledgeable marine electrician. I know that sucks, but I think it will save you heartaches in the end.
It's not possible to diagnose your problem(s) from a distance for several reasons, including your misuse of terms. Battery switches are not "isolators", and I think you're referring to battery switches.
Battery isolators are diode-based devices which, indeed, have a voltage drop across them. This may or may not be related to your problem(s), but based on your description it's hard to tell.
Save yourself some time and, ultimately, expense: get a knowledgeable marine electrician to look at your setup.