Why is my wired keyboard's Eject key no longer working after OS upgrade? Though it sounds like a duplicate of this question, it isn't; the difference is that my eject key works when I connect it to another Mac, so the hardware is good.

The situation is that I have a MacPro3,1 tower with an optical drive that I recently upgraded to El Capitan. The eject key always worked before, but after the move to El Capitan it no longer works and I either have to use the menu bar command or press the physical button on the drive (it is an aftermarket BD-ROM from MacSales).

The keyboard is directly connected to the Mac, no USB hubs or anything in the middle. I have not changed any settings for Fn keys. I do have Karabiner installed to re-map the right-option key for Citrix sessions, but using its "display all keyboard events" tool, it seems that the eject key has no event associated with it. I would have thought this meant it is a hardware issue, but seeing how it worked with no problem on my other Mac, I'm guessing the key isn't mapped like the rest.

Any ideas?
In response to Allan's comments on the original question, I attempted safe mode and found that the eject key still worked and also realized that it worked before I logged in to my account. Obviously, it was something my profile was loading at login time.

While I'm not sure which item specifically helped, I did notice that I had an older "iTunes Helper" and also quitting iTunes (which is normally loaded all the time) did seem to correspond with the eject key working again, but I'm not 100% convinced that it was the precise culprit. While iTunes has always had a helper, I think this particular one might have been an artifact of an older installation that got carried over in the upgrade and caused the problem.