this is more an upstream bug rather than gentoo bug. if pulseaudio isn't used, all sound devices in skype are set to virtual device. according to this link: http://community.skype.com/t5/Linux/No-sound-with-ALSA-after-recent-Skype-upgrade-4-2-gt-4-3-on/td-p/3219164 alsa support was dropped! Reproducible: Always
indeed, skype dropped alsa support!