Ao instalar o Canonical Partner, certifique-se de instalar os pacotes skype e skype-bin. Então, se você usa uma janela de terminal, você precisa:
sudo apt-get install skype skype-bin
Isso deve instalar a versão mais recente (4.3).
Este é um exemplo de atualização do Skype 4.2 para o 4.3:
$ dpkg-query -W skype skype-bin
skype 4.2.0.11-0ubuntu0.12.04.2
skype-bin 4.2.0.11-0ubuntu0.12.04.2
$ sudo apt-get install skype skype-bin
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages will be upgraded:
skype skype-bin
2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 20,1 MB of archives.
After this operation, 5 106 kB of additional disk space will be used.
Get:1 http://archive.canonical.com/ utopic/partner skype-bin i386 4.3.0.37-0ubuntu0.12.04.1 [20,1 MB]
Get:2 http://archive.canonical.com/ utopic/partner skype i386 4.3.0.37-0ubuntu0.12.04.1 [16,1 kB]
Fetched 20,1 MB in 7s (2 828 kB/s)
(Reading database ... 511027 files and directories currently installed.)
Preparing to unpack .../skype-bin_4.3.0.37-0ubuntu0.12.04.1_i386.deb ...
Unpacking skype-bin (4.3.0.37-0ubuntu0.12.04.1) over (4.2.0.11-0ubuntu0.12.04.2) ...
Preparing to unpack .../skype_4.3.0.37-0ubuntu0.12.04.1_i386.deb ...
Unpacking skype (4.3.0.37-0ubuntu0.12.04.1) over (4.2.0.11-0ubuntu0.12.04.2) ...
Processing triggers for bamfdaemon (0.5.1+14.10.20140925-0ubuntu1) ...
Rebuilding /usr/share/applications/bamf-2.index...
Processing triggers for desktop-file-utils (0.22-1ubuntu2) ...
Processing triggers for mime-support (3.55ubuntu1) ...
Processing triggers for gnome-menus (3.10.1-0ubuntu2) ...
Processing triggers for hicolor-icon-theme (0.13-1) ...
Processing triggers for dbus (1.8.8-1ubuntu2.1) ...
Setting up skype-bin (4.3.0.37-0ubuntu0.12.04.1) ...
Setting up skype (4.3.0.37-0ubuntu0.12.04.1) ...
$ dpkg-query -W skype skype-bin
skype 4.3.0.37-0ubuntu0.12.04.1
skype-bin 4.3.0.37-0ubuntu0.12.04.1