Maybe also try to disable hardware acceleration on the gl ui to be extra sure.
Then replace cake with fqcodel (ive readed fqcodel works a bit better than cake on this soc mainly for higher speeds).
then reboot.
Edit:
Also it is likely wed is enabled too (wifi only), wed and SQM is a little complicated topic, one says it bypass sqm, the other tested it fine, + theres also tuning going on by OpenWrt upstream so you might want to play with this setting too and restart.
It is, the issue is after a reboot, then if disable it and enable it again it works, or if I restart it through SSH. I guess the process of the GL firmware is causing the issue, just like you said
Connected using a cable because eth1 is the LAN port, when I test over Wi-Fi SQM doesn't work at all, doesn't shape upload and download.
Hardware acceleration is disabled, I might have forgotten to disable it once while testing yesterday because I tried 4.5.16, 4.6.2 and 4.6.0-op24 but I have the same issue.
If I choose eth0 and apply settings it works over Wi-Fi, shapes both, after the reboot it only shapes download not upload. So, back to the same issue.
I tried to move the startup position and it didn't help, will keep trying.
So, should your script at /etc/init.d/sqm have a /etc/init.d/gl_eqos stop if it's running?
And also the opposite... When you start the gl_eqos, it must check if SQM is running. If yes, then stop it, once both are incompatible with each other.