I did a few GS missions with your app, I noticed a few things :
I put a 1 minute stay tome at one waypoint, that was the max setting of the menu.
followed by a leg of low speed.
The copter stayed at the waypoint for over 3 minutes, then I triggered RTH, I got the confirmation on the app that RTH was initiated, but the copter just turned to home and didn't move. Speed was 0 kph ... So I went to GPS mode and flew home manual.
Then I edited the GS mission, got rid of the stay time and changed the speed back to fast on that one leg, saved the mission, checked every detail in the mission, and tried again.
This time it didn't stop at the waypoint, but the leg with the slow speed was still slow....so the newly saved mission had still older values over riding new ones.
My hunch is that you might have to erase the speed settings first and then add new values (in the code)for changes of GS missions. For the RTH to work, maybe give RTH priority.