Your problem is with the wiring of the Isolator Relay. You should have three wires from the relay and they need to be wired as described in this info. Check to see where each of the three wires go and you probably will find your problem. That red wire is probably to the switch for joining chassis and house batteries for emergency starting in the event your chassis battery is low or dead.
Intellitec's Battery Isolator Relay Delay/E offers a low cost, reliable approach to charging multiple batteries.
Unlike diode isolators, this system provides an engine driven alternator with main battery before connecting the auxiliary battery. This allows the use of self-exciting alternators and lets the engine briefly warm up prior to placing the load of a heavily discharged auxiliary battery on the alternator.
The unit is fully encapsulated in a plastic enclosure for mounting in the engine compartment with two screws. It operates in combination with a conventional continuous duty cycle isolator relay that has been used by a number of vehicle manufacturers. There are three (3) wires to connect to the delay unit: one from an ignition switched 12 volt source, a ground and the isolator relay coil.
It operates by sensing the voltage on the main 12 volt system. When this voltage goes above 13.3 volts for approximately 12 seconds, as happens when the engine is running normally (normal alternator output voltage is approximately 14.4 volts), it will close the isolator relay providing charging current to the auxiliary battery. When the ignition switch is turned off, the relay will open immediately.
If the voltage should drop below 12.0 volts for more than two seconds while the engine is running, the relay will drop out. This might happen when the alternator is not able to supply sufficient current to all the loads and charge the auxiliary battery.
When the main battery voltage rises above 13.3 volts again, the relay will again close in about 2 seconds to retry charging the auxiliary battery. The resultant flicker of the
lights will alert the driver of the system overload.
1988 Fleetwood Limited MH - John Deere Chassis