This happens in both 11.04 and 11.0. I read in some place that this apps are “blacklisted” to explicitly not use overlay scrollbars, but why?
EDIT (17 Sep): Now Update Manager has been whitelisted and it uses overlay scrollbars (see this revision). Synaptic still is blacklisted.
This was actually a bug which was reported on launchpad.net , it was confirmed by the Ubuntu Team and then subsequently fixed.
You can see the history of this bug here:
It has possibly something to do with the fact that they are applications requiring root access. If you run synaptic without administrative privileges, synaptic will join the appmenu. If you run it with admin privileges, it will not. My guess is that these parts of the Ayatana framework require D-Bus-communication from app to shell and backwards. However, communication from System-Bus to Session-Bus seems to be problematic.