Hello! I had this same problem, basically, the media buttons on my Logitech K360 (wireless) wouldn't work at all, tried the fixes proposed here with no success (or partial, like the keys working with SetPoint not running), but then I found a fix that totally worked for me and here it is:
Open your "players.ini" (in your ".../Logitech/SetPointP/" folder), find this part and delete it (read the warning before deleting!):
iTunes_104=wac,xxx,xxx,1,0iTunes=wac,xxx,xxx,1,0
Warning! Notice it's different (shorter) from this part which you DON'T want to delete:
iTunes_104=wac,iTunes.exe,ITWindow,xxx,xxx,xxx,xxx,xxx,xxx,xxx,0,1,iTunes (Don't delete this!)
iTunes=wac,iTunes.exe,iTunes,xxx,xxx,xxx,xxx,xxx,xxx,xxx,0,1,iTunes (Don't delete this!)
If all goes well you should have the media buttons working again with SetPoint on as it should. My guess and how I found this out is that I found it strange to have the iTunes_104 and the iTunes part twice in the ini, so I guessed this shorter version was probably flawed and interfering with the "real" data used by SetPoint.
Wish you all luck! And thanks to those who proposed the initial fixes!