You did not specify which separator you have, I expect Surepower but below are the turn on / off voltages for the Surepower and the Bluesea 762X.
SurePower 1315 :
Connect Voltage 13.2 Volts
+/- 2%(12.96 - 13.46)
Connect debounce 4.4 s
Disconnect Voltage 12.8 Volts
+/- 2% (12.54 – 13.05)
Disconnect debounce 7.2 s
Continuous Duty Relay
Bluesea 7622 :
Relay Contact Position:
-Combine (30 sec.) 13.5 Volts
-Combine (90 sec.) 13.0 Volts
-Open Low (10 sec.) 12.35 Volts
-Open Low (30 sec.) 12.75 Volts
(I have not found a specified accuracy)
Magnetic Latch Relay
Although they both pretty much try to perform the same functions, we can tell that they took different approaches. The SurePower appears to be completely comparator level driven design, they don't specify a hold time , but do have a debounce ciruit. Nothing wrong with this approach, but it would be more susceptible to a transient voltage swing, such as something turning on of off than that of the Bluesea unit.
The Bluesea specifies two hold times for both open and close functions, so this leads us down the path of being not only comparator driven, but also they put a timer function in the equation. They of course also have multiple comparator levels. Their timed function eliminates the need for a debounce circuit, at least in the sense of the one performed by Surepower. The minimum timed event is 10 seconds for a open low voltage. This means that the Bluesea would have to see 12.35 volts for 10 seconds. As you would expect this design would inherently be less susceptible to a transient voltage swings. It should be noted that the turn on/off voltage are measuring what is seen at the terminals of the separator, so take that into account when checking voltage levels for connect/disconnect functions.
Now back to your original question of clicking in the night. As Dave already pointed out checking the ground connection would be one of the first things I would look at. Also we are assuming that when you specify at night that this means unplugged at night, or no external charger.
You also need to monitor and be specific about the state of the batteries as you go into the night, what your power draw is at this time etc. It may be possible that with both battery banks (House and Van) , that if you pulled in and had a very light load that you may go trough a couple of cycles of connect and disconnect, but I would not expect that to happen throughout the night.
A couple of things to help, would be to add an LED across the Surepower relay terminals to monitor when it is on or off. If you have the Bluesea unit the Contura switch #2146 should indicate when the unit is on or off.