Orange and Purple cube odd behavior in auto mode

I use the autopilots on Boat Rovers. The black cube worked similar to the old Gen 1 pixhawks. You flip the switch from manual mode to auto and it starts to follow its course at the speed its set at. Even if the throttle stick is off in manual mode it would run fine once its switch to Auto mode.

The orange cube and now the purple cube seems to behave differently. Once you switch to auto mode ( I use channel 5 on the Futaba) it stops dead. I found if I increase the Throttle at one point it will take off at a high speed. The only way to reign it in is to lower the max throttle to 35% . The problem is, when in manual mode you can only go 35%. Does anyone know of a fix for this?

So basically why does moving the throttle stick even work in Auto mode?