I've been having this problem for a while now, and even though I found a half-patch at some point perhaps someone can tell me how to properly solve it once and for all.
Essentially, certain games and applications (Super Meat Boy, Braid, XBMC) will make the volume go crazy, going up and down more or less at random (although usually tending on the "more" side). After closing the application, if I switch to a console, I'll see the cursor flashing rapidly (something like 5 times per second or so) for a while (while the volume still goes crazy), until both problems stop at the same time (the cursor goes back to normal, and the volume stabilizes).
A patch I've been using is, essentially, running the following script before any app which I know triggers this problem:
xmodmap -e "keycode 122 = 0x0000" xmodmap -e "keycode 123 = 0x0000"
This lines, essentially, are remapping the volume up/down keys to nothing, and that stops the problem from happening, but then again, it also causes my volume keys to stop working.
Can anyone help me understand what is going on here? The only common thread between the applications seems to be the fact that they all make intensive use of graphics. I'm running Ubuntu 12.04 on an HP Notebook, and even though this problem is now happening with Cinnamon, it used to happen already on Gnome 2.