The menu applications, defined in application groups in the desktop customizer, disappears when its group is viewed in tlwebadm. This error seems to be imported from the corresponding webmin CGI code, since it exists in webmin too.
To reproduce: use the standard hconf files, open the application groups page in tlwebadm or webmin, and select the group "Hidden" or "Standard". The list "Applications added to Menu" is empty.
Cannot reproduce the issue for tl-disconnect. It is present for the KDE stuff (which lack a title), but that seems to be a bug in 3.1.2 as well and not a regression. Will double check with Morgan, but I suspect we can move this bug.
It seems the problem is that Morgan had removed the tl-disconnect application, but that doesn't remove it from the application group. We should probably handle that case better, either by blocking the removal or automatically clearing it out of any application groups. Not doing that now though...