Same problem here. I'm using a Logitech M705 and Ubuntu 12.10. The side buttons are recognized as normal left clicks. It would be very great too see this fixed, because I use this buttons in many other programs (Chrome, Firefox, File Manager, Software Center) for browsing and it's really annoying that I have to click the GUI buttons to get back/forward.
My back/forward buttons move screens back and forward and I have configured my mouse wheel left/right to switch tracks with the logitech mouse settings app. Using the Performance Mouse MX and never had any issues.
I have a wireless mouse and Spotify. When you are using Spotify some mouse buttons (as the scrolling button or 4 and 5 buttons) may change to control Spotify instead of controlling the PC scrolling up/down or back/forward. I found that if I press for 3 seconds the DPI button on my mouse it continues to control normal the PC functions.
If I press DPI button again for 3 seconds it changes again to media mode and continues to control Spotify.