Right, back from work and here's the rest of it.

The script, ekos_controller.py was put together by another member here, I can't remember who off the top of my head but it was another thread about dbus from quite a while back; I've gone through it, found no noticeable errors in it, rebuilt it a couple of times to make sure and matched it up to the scriptable functions in scheduler.cpp

On the machine, the configuration is a Pi4B 8GB, with the indiserver set to remote though on the same machine to maintain the current settings should kstars go down, the profiles in ekos are set to auto-connect.

The sequence which worked on 3.5.3, was from the terminal (or ssh, or shell script); examples assume relative to desktop.
The CurrentSequence.esl is just a copy of whatever the sequence I am working on at that time.

cd ~/Desktop;
./ekos_controller.py --start_ekos;
./ekos_controller.py --load_schedule ./CurrentSequence.esl;
./ekos_controller.py --start_scheduler;

However on 3.5.5 (and 3.5.7b) using the same python script, the process is :
cd ~/Desktop;
./ekos_controller.py --start_ekos;
./ekos_controller.py --profile 'Default';//Or other server profile name, sometimes fails to connect to the indi control panel
./ekos_controller.py --load_schedule ./CurrentSequence.esl;//Usually will not load correctly, marking as invalid, omitting co-ordinates, job status and .esq sequence count
./ekos_controller.py --stop_scheduler;//To mark the job aborted instead of invalid and allowing to reset
./ekos_controller.py --reset_scheduler;//Here resetting the the schedule sequence to correctly load co-ordinates and .esq file
./ekos_controller.py --start_scheduler;//Restarting the scheduler

This, however, only goes so far to start the scheduler, but when the schedule is started in this manner even with a valid job in the queue, it doesn't select the job and start.

Starting and running a sequence by direct input doesn't cause the same issue to appear. 

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