Installing linux-headers-3.9 onto a system that has alsa-headers-1.0.25 installed results in the following collisions: Detected file collision(s): /usr/include/sound/asequencer.h /usr/include/sound/asound.h /usr/include/sound/asound_fm.h /usr/include/sound/compress_offload.h /usr/include/sound/compress_params.h /usr/include/sound/emu10k1.h /usr/include/sound/hdsp.h /usr/include/sound/hdspm.h /usr/include/sound/sb16_csp.h /usr/include/sound/sfnt_info.h
media-sound/alsa-headers is not in the Portage tree, you'll want to remove it.
Ahh, my bad. Removing it allows linux-headers-3.9 to install correctly. :-)