Do those keys you're having trouble with work with other applications for you?
My case: my keyboard only have 3 media keys: mute and volume +/-. Those work fine. I have two remote controls with media keys. With one of them the media keys work fine while smplayer has the focus but some of the keys (play, pause, rewind, forward) don't work while smplayer is in the background. With the other remote control all keys work fine even when smplayer doesn't have the focus.
The problem with the first remote control is that the driver (I guess) doesn't report the keystrokes for those keys as normal key press events (they are reported as "appcommand" events). I can't find a way to grab those events to use as global shortcuts.
I installed VLC and it can't recognize those keys.