At least, on Ubuntu 22.04.1
I did a lot of googling and the only thing to even mention this was half a blog post on google (the other half was behind a dead link, so I only got a hint of a solution from it).
I am making this post in case someone else runs into this issue.
I ssh'd into my headless server in my admin account. I created a new user for running the service that I wanted to install. I installed the service as a flatpak, ran it as my admin user, and it worked fine. su'd into my service user, and it broke.
The error message was
Note that the directory '/home/user/.local/share/flatpak/exports/share' is not in the search path set by the XDG_DATA_DIRS environment variable, so applications installed by Flatpak may not appear on your desktop until the session is restarted. error: Unable to allocate instance id Searching this turned up hardly anything. Every response was just "reboot your computer", and while that worked for many others that did not solve my issue.
The only way to fix this problem was to sign in as the user directly, not through su
I believe the issue was caused by the environmental variable XDG_DATA_DIRS not being properly set. On login, it is set to a directory in your user's home. When you su into another user, it is not updated and stays as the original user.
I hope this post saves someone the headache that I experienced from this.
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