There are basically 3 times something types of isolators..
Basic Diode isolators
Improved diode isolators
Solenoid/contactor/relay based isolators (Best)
With the basic.. These are designed to be used with an alternator, if the alternator is putting out say 14 volts. the batteries may see as little as 12, this is not enough to fully charge them (NOTE I am using round figures here) a good diode isolator may only drop a few tenths of a volt.
In improved isolator has a 3rd circuit.. this is to feed the vehicle or charger's voltage regulator.. HOWEVER not all alternators and darn few converters know what to do with that signal My Alternator for example has an internal voltage regulator and there is no way to feed the reduced voltage to it.
Solenoid type.. Do not have this issue.