it happens to me, too, but I do not immediately understand why and I need to dig deeper. In the meantime, here's a workaround. Run the following commands in the console at the bottom of the IDE:
mkdir -p /opt/Bela/local/;
printf '#!/bin/bash\ncd /root/Bela/projects/$PROJECT\n./$PROJECT\n' > /opt/Bela/local/bela_startup.sh;
chmod +x /opt/Bela/local/bela_startup.sh;
then reboot. Does it work now?
If you ever want to remove this workaround (which is needed e.g.: if you want to run supercollider or csound projects at boot), simply run
rm -rf /opt/Bela/local/bela_startup.sh once.