2 hours ago I installed Ubuntu while listening to music on my headphones (wubi install). I then also played music on Ubuntu just fine, yet when I rebooted into Windows, without doing anything else besides opening Chrome, my headphones stopped working.
Exact same problem as in this thread: headphones not working on Windows after installing Kubuntu 12.10, which was left with many doubts and no answer.
Luckily I have not done anything on windows after installing Ubuntu 12.10, nor have I mingled with the audio driver. I fixed the problem using some advice from a discussion thread by rebooting into Linux and forcing the laptop to shutdown by holding the power button (in order to prevent Linux from muting the headphone jack in a way that Windows doesn't see). The headphones now work like before, thus it is obviously a problem originating from Linux.
Although this trick works for now, and I assume that it will work as long as I never shutdown Linux properly, I would definitely like a proper solution to this.
The discussion thread where I was told to crash Linux: https://bbs.archlinux.org/viewtopic.php?id=146773