I have no experience with makerbot software. However in replicatorg, onboard preferences, there is a button to click that says "override Gcode target temperatures". Perhaps there is something similar in your software. Make sure that you go through all your possible settings to ensure that there isn't an option that is overriding your target temperatures. Also on my flashforge creator pro I can change the nozzle temps by using the LCD controls to up the temp to where I want it.

Other than that how do you like Makerbot software? I'm using sailfish firmware and replicatorg and I feel like im trying to learn how to decode the freakin``