I'm having the same issue (with most games).  How I fixed the issue before (specifically with Skyrim) was to uninstall the game, wipe the directory out completely (some mods will leave behind files), and reinstall WITHOUT installing any mods. 

I thought originally that a reinstall fixed the issue, but then I recently tried to play again on my tablet, and no mouse buttons... it's odd because the buttons work on the desktop, and the buttons work in the Diablo III beta... but no mouse buttons work in Skyrim, The Legend of Grimrock, or Superbrothers: Sword and Sworcery. 

I have the same problem when in full screen (and I have an Nvidia card, so full screen *should* be supported). However, both mouse buttons work if I run Skyrim in windowed mode. I suggest you try that.