That's strange then, I believe Electron just calls xdg-open and there's not much more to it than that; I'm curious, could you try extracting the AppImage to expose the raw Joplin binary and invoke the binary directly; just incase the AppImage itself is changing your environment ever so slightly that might be causing this.
There's a handy script here that might help; Extracting appimage to improve io/cpu startup performance - it's unsupported because the majority of people won't be doing it, but it's not risky in the sense of data loss, just the potential weird edge case issues. It would be interesting though if the discussion in that thread is the root cause of your problem here, i.e, I'm suspicious the AppImage changing the $XDG_DATA_DIRS could be related.