G'day 2 rocks,
I don't think there is a problem in your duel battery sytem.
The isolator allows the second battery to charge while the engine is runing(uses an ignition feed, so fuel/starter in laymans terms).
When the motor is turned of it "isolates" the 2nd battery to allow you to use it without affecting the starting battery.
This way you can run your air compresor/fridge/ lights off the 2nd batt till the cows come home with out fear of running the starting battery flat.
It apears to me your starter batt is not right, might have just got flat when you did the work(inside light on ect.).
Give it a charge and get it tested after checking all the terminals and lead mounting points.



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