Apt doesn't know about the %OSGEO4W_MENU_LINKS% and %OSGEO4W_DESKTOP_LINKS% variables introduced in setup.exe v1.0.6-5.
With the qgis-dev package this manifests with a mkdir was unexpected at this time. error message at the console during postinstall phase, consequently the Start Menu and Desktop shortcuts are not created, nor are the relevant registry entries created/updated.
http://trac.osgeo.org/osgeo4w/ticket/300