This is a longstanding issue with the org.freedesktop.FileManager1 protocol; see 397953 – KIO::highlightInFileManager does not respect default file manager setting when launched via FileManager1 DBus activation. If it was working properly for you in the past despite having Thunar installed, this was pure chance.
Until the issue is fixed, you can work around it in any of the following ways:
- Uninstall file managers that aren’t your preferred default file manager.
- Run
dolphin --daemon. Some distros like Fedora do this automatically to work around the bug.