Dear Maintainer,

*** Reporter, please consider answering these questions, where appropriate ***

   * What led up to the situation?
updatet Debian 12 to Debian 13
   * What exactly did you do (or not do) that was effective (or
     ineffective)?
package-update-indicator lives in the Xfce4-panel and starts automatically
   * What was the outcome of this action?
after a few days there was no notification of updates, so I tried `sudo apt update` and found several updates that were not shown by package-update-indicator
   * What outcome did you expect instead?
blue star in the panel turnig orange or red indicating there were package-updates to install

Logs:
olaf@thinkpad:~$ sudo apt update
[sudo] Passwort für olaf:
OK:1 https://deb.debian.org/debian trixie InRelease
Holen:2 https://deb.debian.org/debian trixie-updates InRelease [47,1 kB]
Holen:3 https://deb.debian.org/debian trixie-backports InRelease [53,5 kB]
Holen:4 https://security.debian.org/debian-security trixie-security InRelease [43,4 kB]
Holen:5 https://deb.debian.org/debian trixie-backports/main amd64 Packages [724 B]
Holen:6 https://packages.element.io/debian default InRelease [3.618 B]
Holen:7 https://deb.debian.org/debian trixie-backports/main Translation-en [1.016 B]
Holen:8 https://security.debian.org/debian-security trixie-security/main amd64 Packages [20,5 kB]
Holen:9 https://security.debian.org/debian-security trixie-security/main Translation-en [14,3 kB]
Holen:10 https://packages.element.io/debian default/main amd64 Packages [1.078 B]
Es wurden 185 kB in 0 s geholt (410 kB/s).
Aktualisierung für 6 Pakete verfügbar. Führen Sie »apt list --upgradable« aus, um sie anzuzeigen.
olaf@thinkpad:~$ pkcon refresh
Zwischenspeicher wird aktualisiert      [=========================]
Zwischenspeicher wird geladen           [=========================]
Aktualisierungsinformationen werden heruntergeladen[=========================]
Ausführen                              [=========================]
Fertig                                  [=========================]
 Aktiviert                            https://security.debian.org/debian-security trixie-security InRelease
 Aktiviert                            https://deb.debian.org/debian trixie InRelease
 Aktiviert                            https://deb.debian.org/debian trixie-updates InRelease
 Aktiviert                            https://security.debian.org/debian-security trixie-security InRelease
 Aktiviert                            https://deb.debian.org/debian trixie-backports InRelease
 Aktiviert                            https://deb.debian.org/debian trixie InRelease
 Aktiviert                            https://packages.element.io/debian default InRelease
 Aktiviert                            https://deb.debian.org/debian trixie-updates InRelease
 Aktiviert                            https://deb.debian.org/debian trixie-backports InRelease
 Aktiviert                            https://packages.element.io/debian default InRelease
olaf@thinkpad:~$ pkcon get-updates
Aktualisierungen werden abgerufen       [=========================]
Zwischenspeicher wird geladen           [=========================]
Fertig                                  [=========================]
Sicherheit  	chromium-139.0.7258.138-1~deb13u1.amd64 (debian-stable-security-main)	Webbrowser
Sicherheit  	chromium-common-139.0.7258.138-1~deb13u1.amd64 (debian-stable-security-main)	Webbrowser - gemeinsam genutzte Ressourcen der Chromium-Pakete
Sicherheit  	chromium-l10n-139.0.7258.138-1~deb13u1.all (debian-stable-security-main)	Webbrowser - Sprachpakete
Sicherheit  	chromium-sandbox-139.0.7258.138-1~deb13u1.amd64 (debian-stable-security-main)	Webbrowser - isolierter »setuid«-Bereich (sandbox)
Sicherheit  	firefox-esr-128.14.0esr-1~deb13u1.amd64 (debian-stable-security-main)	Webbrowser Mozilla Firefox mit verlängerter Wartung (Extended Support Release, ESR)
Sicherheit  	firefox-esr-l10n-de-128.14.0esr-1~deb13u1.all (debian-stable-security-main)	Deutsches Sprachpaket für Firefox ESR
olaf@thinkpad:~$ package-update-indicator --quit
olaf@thinkpad:~$ package-update-indicator --debug

(package-update-indicator:2672): libayatana-appindicator-WARNING **: 18:49:44.261: libayatana-appindicator is deprecated. Please use libayatana-appindicator-glib in newly written code.
(package-update-indicator:2672): package-update-indicator-DEBUG: 18:49:44.417: property "update-command" set to "/usr/bin/gpk-update-viewer"
(package-update-indicator:2672): package-update-indicator-DEBUG: 18:49:44.417: property "always-active" set to "TRUE"
(package-update-indicator:2672): package-update-indicator-DEBUG: 18:49:44.418: indicator icon: system-software-update, notification title: "", notification body: ""
(package-update-indicator:2672): package-update-indicator-DEBUG: 18:49:44.419: indicator icon: system-software-update, notification title: "", notification body: ""
(package-update-indicator:2672): package-update-indicator-DEBUG: 18:49:44.425: backend: apt
(package-update-indicator:2672): package-update-indicator-DEBUG: 18:49:44.425: roles: cancel;depends-on;get-details;get-files;get-packages;get-repo-list;required-by;get-update-detail;get-updates;install-files;install-packages;install-signature;refresh-cache;remove-packages;repo-enable;resolve;search-details;search-file;search-group;search-name;update-packages;what-provides;download-packages;get-old-transactions;repair-system;get-details-local;get-files-local;repo-remove
(package-update-indicator:2672): package-update-indicator-DEBUG: 18:49:44.425: network-state: online
(package-update-indicator:2672): package-update-indicator-DEBUG: 18:49:44.426: property "refresh-interval" set to 86400
(package-update-indicator:2672): package-update-indicator-DEBUG: 18:49:44.426: property "use-mobile-connection" set to false
(package-update-indicator:2672): package-update-indicator-DEBUG: 18:49:44.427: state initial -> up-to-date
(package-update-indicator:2672): package-update-indicator-DEBUG: 18:49:44.427: indicator icon: system-software-update, notification title: "Auf dem neuesten Stand", notification body: "Das System ist auf dem neuesten Stand"
(package-update-indicator:2672): package-update-indicator-DEBUG: 18:49:44.438: setting HTTP proxy to "(null)"
(package-update-indicator:2672): package-update-indicator-DEBUG: 18:49:44.438: setting HTTPS proxy to "(null)"
(package-update-indicator:2672): package-update-indicator-DEBUG: 18:49:44.438: setting FTP proxy to "(null)"
(package-update-indicator:2672): package-update-indicator-DEBUG: 18:49:44.438: setting SOCKS proxy to "(null)"
(package-update-indicator:2672): package-update-indicator-DEBUG: 18:49:44.438: setting the list of download IPs which should not go through a proxy to "(null)"
(package-update-indicator:2672): package-update-indicator-DEBUG: 18:49:44.438: setting the PAC string to "(null)"

*** End of the template - remove these template lines ***

There is an initial delay before the first check is performed, could you
let it run for a couple of minutes and see if there is any more output?

Thanks,

I've updated to trixie and package-update-indicator does show available
updates in GNOME with the gnome-shell-extension-appindicator addon, so
this issue must be Xfce-specific.

This rather seems to be a machine-specific misconfiguration, maybe caused by the update from bookworm to trixie.
Updates are shown as expected by package-update-indicator in a freshly installed trixie with Xfce on another computer.