Try using it on another pc and that'll proove whether it's the mouse or just the drivers. Perhapse you did not uninstall them correctly. If it's fine on another pc without razor drivers, then use Revo to uninstal the drivers and then reinstall the newest drivers.
I don't know how the Razor Naga works, but with my G9x, you can create different profiles. Perhaps something accidentally disabled the button in one profile?
dude had a similar issue. Here's what he did to fix it:
download the latest firmware update from the site i believe its 1.13 its just the installer and not the actual firmware update to update your mouse...
1. go into progams/razer/naga/firmware updater
2. disconnect ur mouse and hold the left right and mouse 3 buttons then reconnect ur mouse and click next on the screen (it should detect your mouse and start its update)
3. after installer is done it asks you to replug your mouse in plug it back in and it should work fine all ur keybindings that u have on ur software should work and be able to use