N-mosfet to disconnect voltage regulator causes wrong V_OUT
I can't follow the circuit very well either, 

but I guess you are trying to disconnect the ground of the power switch using the N-Ch. 

R8,R9 are dividing the gate voltage, but you probably need 6V on the gate to turn the N-ch on properly. i.e max9015 needs 24V supply to get enough Vgs

I can't really understand the circuit. Your opamp seems to be powered by the output of the switchmode it is turning off. You are using a fet for some reason, when the LTC has a shutdown pin. 

Your question really needs a lot of editing to make sense....