Sounds as though your battery isolator is permanently isolating; troubleshoot that circuit. Often it's basically a solenoid (as in a heavy-duty relay) which is switched in at the appropriate times. The problem could be this solenoid unit itself, or the control wire/logic to turn it on, or a fuse in the line, or a connection at either end...
Sometimes the isolator is not a solenoid but a heavy-duty diode device. Similar troubleshooting applies, though some of the specific details are a bit different.