If I read you right...you have always had negative from main battery disconnected when using second yes?...if so that terminal could be carrying the main negative to engine and you might find your not getting a good enough return to battery...on my 101 the earth goes from.battery to starter so.
 
Disconect clamps from main and put a meter across pos and neg on main removed clamps not on the connectors the clamp bodies..
 
If I read you right...you have always had negative from main battery disconnected when using second yes?...if so that terminal could be carrying the main negative to engine and you might find your not getting a good enough return to battery...on my 101 the earth goes from.battery to starter so.
Yes, the neg is disconnected from battery 1 since I want to use only battery 2, but the same earth connections (from battery 1 to starter etc) are in use. Also, I added 2 jumper cables directly to the chassis and that didn't help either, but I guess you are right. I will have to connect battery 2 to the starter directly. Wiring it through battery 1 does not work for some reason.
 
No...set meter to 24v then probe neg and pos from clamps removed from main battery with isolater closed should give a strong 12+v reading if not you've a faulty connection from second battery
 

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