I may have the same problem. With steam minimized, using right pad, controller makes sounds and I think the pointer actually moves, but the cursor (meaning the arrow on screen) stays at one place. Can you try move it over some 'hoverable' element (like tab in browser, or hyperlink) and see if it reacts?
This isn't reproducible with modern Big Picture Mode
Closing as per the last comment.
Nothing extracted yet.
In Big Picture Mode, pressing "Minimize big picture" shows the desktop, but Steam-controller mouse emulation doesn't work.
In that state, moving the analog-stick makes a sound, so I think it actually still controls Steam (BPM) even though it's minimized.
Pressing Steam-button on the Steam-controller returns to BPM.
A different way to minimize BPM (that works fine) is to press Alt+Tab, but that's not possible when I play in front of the TV, away from a physical keyboard.
OS: Kubuntu 15.10 (x86_64)
Running Steam client beta:
Steam client built: Dec 10 2015, at 11:39:41
Steam versions: 1449778863
system_information.txt