Media Keys Not Working for a Specific User Account
So I typed this whole thing out and the culprit presented itself right after I posted it!

I have a trackball by Elecom, love it, but apparently there was a problem with their Elecom Mouse Assistant software; an error message popped up, so I force quit it, trashed its settings and relaunched it, and now my media keys are fine again.

It must have something to do with the ability to remap the mouse buttons to various functions (volume and media functions being some of them).

For anyone that experiences the same problem, and has Elecom Mouse Assistant installed, you may wish to try:


Relaunch the app:


Open mouse assistant (from System Preferences)
Make a minor change (e.g- assign a mouse wheel click function), and click Apply.
Check your media keys, this may have resolved your issue.
If necessary, re-open mouse assistant and change your settings back to the way you wanted them.

If that doesn't work, you may try the following:


Locate your settings file and delete it. This appears to be a hidden XML file stored under your user directory, so it will most easily be found using Terminal:
Open Terminal.app
Enter the following command and hit enter: ls -al
Look for a strangely named file with the .xml extension. I'm not sure of the naming convention, it may be model specific, but mine is: .VID056e_PID00fc.xml
Remove the file using the rm command, substituting in the correct name for the file, like so: rm ~/.VID056e_PID00fc.xml
Logout of the user account, and then log back in again



Using either option your normal use of your media and volume keys should be restored without having to uninstall mouse assistant.

I won't mark this as the right answer, but may leave the question in place in case anyone else has the same issue, or has other causes they would like to document for others.