One thing to note is: you can only have once instance of the updater running. i.e. you cannot do a apt-get on the command line and also use synaptic at the same time --- although you should see an error if you try.
You could try making sure your sources are correct. Type, $ sudo gedit /etc/apt/sources.list
make sure the sources read the following - if you are on 5.10 (breezy badger)
deb
http://archive.ubuntu.com/ubuntu breezy main restricted
deb-src
http://archive.ubuntu.com/ubuntu breezy main restricted
deb
http://archive.ubuntu.com/ubuntu breezy-updates main restricted
deb-src
http://archive.ubuntu.com/ubuntu breezy-updates main restricted
deb
http://archive.ubuntu.com/ubuntu breezy universe
deb-src
http://archive.ubuntu.com/ubuntu breezy universe
deb
http://security.ubuntu.com/ubuntu breezy-security main restricted
deb-src
http://security.ubuntu.com/ubuntu breezy-security main restricted
deb
http://security.ubuntu.com/ubuntu breezy-security universe
deb-src
http://security.ubuntu.com/ubuntu breezy-security universe
deb
http://archive.ubuntu.com/ubuntu breezy multiverse
deb-src
http://archive.ubuntu.com/ubuntu breezy multiverse
deb
http://archive.ubuntu.com/ubuntu breezy-backports main restricted universe multiverse
Save the file and type: $ sudo apt-get update
then try run the package program again - if it does not work still, try and do a apt-get install... a random program can be '3ddesktop' > it is a cool program anyway
$ sudo apt-get install 3ddesktop
