I'm having this issue on just one of my computers, sadly the one on which I do most of the gaming.
The side buttons worked just fine when I first installed CUE, but after the next reboot they failed. I also noticed that it's not just the side buttons that are affected, none of the buttons will trigger a programmed command. Reinstalling CUE seems to be a temporary fix for me, but hardly an acceptable one at that. Also the application sometimes decides to just randomly hang whenever switching profiles or closing.
I attached a log file, strangely it looks pretty much identical to the ones from my laptop where everything seems to be working just fine. 2016-01-20T07-10-53.txt.txt