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.