In the Applications menu, GNU Emacs is under Accessories but XEmacs is under Programming tools. They should be consistent.
xemacs-21.5.29-6.fc11 has been pushed to the Fedora 11 testing repository. If problems still persist, please make note of it in this bug report. If you want to test the update, you can install it with su -c 'yum --enablerepo=updates-testing update xemacs'. You can provide feedback for this update here: http://admin.fedoraproject.org/updates/F11/FEDORA-2009-11027
xemacs-21.5.29-6.fc11 has been pushed to the Fedora 11 stable repository. If problems still persist, please make note of it in this bug report.