I'm having the exact same issue (after rolling back the audio driver
due to not having the ability to enable speakers that appeared to have been disabled by the "update"). It's not just one program. It's everywhere and yes, the headphones are being recognized and Vista claims they are working.
Setting the speakers to default, restarting the system, trying to re-install the update and disabling the speakers entirely (each one seperately or in combination) have all resulted in the same end: sound from the speakers while the headphones are connected and no sound from the headphones themselves.
I would post this as a new thread, but the previous reply was.. well, obviously of no assistance.