After upgrading to the 3.9 kernel on F18, the headphone jack on my laptop stopped working (Intel HD audio: VIA1802 and Intel PantherPoint HDMI are listed as the codecs). This seems to be a 3.9 kernel problem and not specific to F18. I had no issues on the 3.8 kernel and there are similar reports for other distros, all pointing to the 3.9 kernel as the issue.
What I did to fix the problem:
1. Run alsamixer from a console
2. Select F6 and select the specific sound card ("0 HDA Intel PCH" in my case)
3. Right-arrow over to "Auto-Mute Mod" and hit the down arrow to set it to "Disabled"
4. Hit escape to exit
5. Save the ALSA configuration with: su -c "alsactl store" (or sudo alsactl store)
For whatever reason, "Auto-Mute Mode" is enabled and causing the problem.
What I did to fix the problem:
1. Run alsamixer from a console
2. Select F6 and select the specific sound card ("0 HDA Intel PCH" in my case)
3. Right-arrow over to "Auto-Mute Mod" and hit the down arrow to set it to "Disabled"
4. Hit escape to exit
5. Save the ALSA configuration with: su -c "alsactl store" (or sudo alsactl store)
For whatever reason, "Auto-Mute Mode" is enabled and causing the problem.