Hey Mate,
Just wondering, what battery protection setting have you got your Waeco on? I reckon where you're running into trouble is that you've got your fridge on the highest battery protection setting and it's stopping operation because of that.
Your Waeco fridge will have three levels of battery protection, high medium and low. This is so that you can use your fridge in a few different scenarios.
High - if you're running the fridge on your starter battery, and want to be able to start as your highest priority.
Medium - if you're running the fridge on your starter battery, or second battery where protecting your battery health is important but starting is not critical.
Low - if you're running the fridge on a isolated second battery, and you want your fridge to run as long as possible.
IMO - I would change it to the LOW setting, as the reason you have a fridge with a second battery is to run it as long as possible. I would avoid allowing the fridge to fully discharge the battery wherever possible however.
If I was you, I would go to Jaycar and buy yourself a cheap $20 voltimeter. That will help you tell if your battery has any charge left in it or not.
Hope this helps,
Jon