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I also found the same behavior using the amd64 version (2.2.0.35-1) downloadable directly from Skype.  
http://www.skype.com/go/getskype-linux-beta-ubuntu-64 

I'm back to the skype:i386 for now as that seems to be the preference
now with multi-arch.

Recently a broken amd64 skype appeared in the the Natty partner archive.
This one just plain doesn't work, but is easily installable creating a
separate issue people trying to figure out notification issues might
trip over.  It is tempting since it cleans up all the i386 multi-arch
packages.

apt-get install skype:i386 if you end up executing the following (note I
use the simulate flag -s below)

root@oneiric:~# apt-get install skype -s
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following packages were automatically installed and are no longer required:
  libkrb5-3:i386 libk5crypto3:i386 libstdc++6:i386 libqt4-declarative:i386
  liblcms1:i386 libqt4-script:i386 libqt4-network:i386 libqt4-dbus:i386
  libgnutls26:i386 libtasn1-3:i386 libfreetype6:i386 libexpat1:i386
  libqt4-xmlpatterns:i386 libavahi-common-data:i386 libxcb1:i386 libxau6:i386
  libpanel-applet-4-0 libcups2:i386 libqtcore4:i386 libkrb5support0:i386
  libice6:i386 libxdmcp6:i386 libgcrypt11:i386 libkeyutils1:i386
  libqt4-sql:i386 libasound2:i386 libxrender1:i386 libqt4-xml:i386
  libxss1:i386 libtiff4:i386 libjpeg62:i386 libqtgui4:i386
  libavahi-client3:i386 libx11-6:i386 libfontconfig1:i386 libsm6:i386
  libgssapi-krb5-2:i386 libxi6:i386 libaudio2:i386 libxt6:i386 libxv1:i386
  libxext6:i386 libavahi-common3:i386 libmng1:i386 libgpg-error0:i386
Use 'apt-get autoremove' to remove them.
The following packages will be REMOVED:
  skype:i386*
The following NEW packages will be installed:
  skype
0 upgraded, 1 newly installed, 1 to remove and 0 not upgraded.
Purg skype:i386 [2.2.0.35-0natty1]
Inst skype (2.2.0.35-0natty1 Partner archive:11.04/natty [amd64])
Conf skype (2.2.0.35-0natty1 Partner archive:11.04/natty [amd64])

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Partner Developers, which is subscribed to skype in Ubuntu.
https://bugs.launchpad.net/bugs/845173

Title:
  Missing system tray icon

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