This autoit script, and accompanying reg file seem to work for updating reader automatically when compiling and calling from the login script. It also deletes some of the speed loader crap that adobe turns on. The updater checks the registry for the last updated date and if it's more than 3 days ago, runs the update check (inherent in the updater).
Attached are the au3 file and reg file as text files. You could probably do away with the reg file and use reg.exe to create the entry, but I knew it works this way and didn't want to mess with it.
I'd like to figure out some way to get someting similar going on java if anyone has any ideas. Like someone said above though, even if it's set to auto download, there's no obvious setting to auto install inherent in the updater.
http://goo.gl/vrvqC
Update: For java, try downloading the offline version and using the switches with a run-as admin acount similar to above:
http://www.java.com/en/download/manual.jsp
http://www.java.com/en/download/help/silent_install.xml