I'm using a Logitech Y-BN52 and it doesnt work with SetPoint (v6.61) running in the background. I guess they just don't cohere with one another. If I exit SetPoint, everything works but you don't get to use the other features that SetPoint offers on your keyboard, which is pretty much a trade-off.
edt: also found this information from a logitech support forum
" Since MusicBee, VLC and Mediamonkey are based upon web applets (flash, java script) and are not an application like the Windows Media Player, the keys on your Logitech Wireless Combo MK520 can't be able to change parameters like prev, play/pause, next, and media information "can't be understood" by the keyboard since it is based on flash, therefore you're unable to use the media keys with these programs."
different keyboards models, same brand, and same keyboard software (SetPoint)
source:
http://forums.logitech.com/t5/Keyboards-and-Keyboard-Mice/KM520-media-keys-not-working-globally/td-p/942114