I have the same problem and just checked my Volume Control under Xubuntu 12.04 
LTS on my Thinkpad Edge. There are two ports under "Output Devices", namely:
- HDMI / Display Port
- Analogue Output
Using the Fn keys only changed the HDMI output, but not the Analogue Output. 
Now after a playing around for a while the keys don't work any more at all. 
Still, might the problem be related to the different output channels?

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https://bugs.launchpad.net/bugs/990562

Title:
  Laptop FN Sound Keys don't update mixer volume

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