When I upgraded the kernel to 3.9, for some reason I get no sound through the headphones, but the speaker works fine. I went through the typical troubleshooting steps, e.g. editing /etc/modprobe.d/50-sound.conf, with no luck. So I tried the earlier kernel and much to my surprise, it worked!
I did an lsmod on both kernels and they both have the same modules loaded, though as expected the 3.9 modules are of different sizes.
I suspect there is an issue with the drivers, but I really don't know how to procede at this time. My sound card/mixer settings are OK because everything works with kernel 3.8; the ONLY difference is the kernel and some of the modules.
I have the ICH9 chipset.
Here is the output of the ALSA debug:
3.9 Kernel
http://www.alsa-project.org/db/?f=7ce3c0a19dde078619a3c16bb8fce1f861226679
3.8 Kernel
http://www.alsa-project.org/db/?f=1b5e4d7aaf024caed25c47f6f9c7645608ad5106
I have a bug opened with ID 818828
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Edward Reiss