You should set Cura to reprap gcode flavor in the printer settings. That may solve the issue, though reprap firmware does accept the Marlin gcodes for speed, acceleration, and jerk now, so it shouldn't matter.
What firmware version are you using?
It sounds like you have the part cooling fan plugged into Fan port 1 maybe? It should be plugged into Fan port 0 since the slicers all tend to not specify the fan number, so having it on port 0 just makes it easier. Fan port 1 is defaulted to be the hotend fan and it will spin up briefly at power on.
https://duet3d.dozuki.com/Wiki/Connecting_and_configuring_fans