3 axle break controller issues

I have no idea why your set up won't work but you don't want to do it like that anyway. You need a separate brake controller for each trailer. Use the built in for your first trailer and install an aftermarket one for your second trailer. You will need to adjust each independently to get everything to stop straight.

Incidentally, having more brakes connected does not increase the resistance (assuming you wired it properly) it will actually decrease the resistance causing the brakes to draw more current than what 2 brake axles would.