zypak-wrapper does not find package identifier

[koeppl]

I have installed flatpak with the official installation guidelines on Debian 12, and used flatpak to install packages in user space (via --user).
In my setup, it seems that those packages fail to start that use zypak-wrapper to execute the application in the sandbox environment.
According to flatpak --user repair, there seems no problem with the installation.

If I run flatpak --user run -vv com.slack.Slack, the last lines are as follows.

F: Running 'bwrap --args 35 -- com.slack.Slack'
error: app/com.slack.Slack/x86_64/stable (commit 8ba793f4b579b7b53fa830930e91735c8398d698f873b919eb49cd1b0e342780) not installed
[4 preload-host-spawn-strategy] Failed to let stub process know of exit: Bad file descriptor (errno 9)

I am able to enter shell mode via
flatpak --user run --command=bash com.slack.Slack,
but running zypak-wrapper /app/extra/slack gives the same error message.
It seems that the identifier app/com.slack.Slack/x86_64/stable should be somewhere registered in a table zypak-wrapper wants to lookup, but I am unable to find that information.

The output of flatpak list is as follows.

Name                   Application ID             Version                  Branch      Installation
Slack                  com.slack.Slack            4.41.105                 stable      user
...

I can successfully run flatpak applications such as org.mozilla.firefox or com.adilhanney.saber,
but seemingly none that work with zypak-wrapper such as slack or net.cozic.joplin_desktop.

[d10sfan]

Also seeing a similar problem.