Problem
The Start at login option in OpenDeck settings does not work when OpenDeck is installed via Flatpak. This is actually mentioned in the tooltip of the option itself in the settings panel.
Solution
You need to add OpenDeck to your desktop environment's autostart configuration manually.
Most desktop environments have built-in tools for this — for example System Settings → Autostart in KDE Plasma, or GNOME Tweaks → Startup Applications on GNOME. For other desktop environments, refer to your DE's documentation.
Regardless of which method you use, the important thing is to make sure the Exec= line contains the --hide flag at the very end:
Alternative — Terminal only (all desktop environments)
If you prefer, you can create the autostart file manually regardless of your DE:
Paste the following content:
Save with Ctrl+O then Ctrl+X.
The --hide flag launches OpenDeck directly in the background without showing the main window. OpenDeck will be available in the system tray as usual.