I created two merge proposals...
1) gnome-panel - https://code.launchpad.net/~albertsm.../+merge/215275. With this one alacarte will use correct menu file in gnome-flashback-session. You can manually apply this fix:
Code:
sudo gedit /usr/share/applications/gnome-panel.desktop
Replace this line
with this
Code:
Exec=env XDG_MENU_PREFIX="gnome-flashback-" gnome-panel
2) alacarte - https://code.launchpad.net/~albertsm.../+merge/215284. This will fix new menu and/or item creation. If you are using x64 I can upload deb package with this fix.