@andmaster I have mycontroller starting via crontab and this always works for me, you could try that and see how it works for you. Here on pi3 it is working no problem and every reboot mycontroller comes right back up.
If you can I would recommend replacing the SD card with a SSD HDD. They are quite cheap now (less than £20 in UK) and seem much faster and more stable. I have mine connected to pi via usb adaptor and it is working well.
Another thing to keep in mind is that a good quality power supply and good thick cable from power supply to raspberry pi are strongly advised. Pi seems to be affected by power quality easily. I have been around the block a few times with this!