After doing some recordings, the capture agents randomly starts failing to start capturing, and taking a look at the logs we see that this happens because the audio device fails to initialize. When trying to use external programs we get the message "Device is busy". In the logs we just get the "Unable to start pipeline after 5 seconds. Aborting..." message, and also "alsasrc0: Couldn't initialize device". There is no way to access the device until we stop or restart matterhorn. Then the device starts working normally again.
With lsof we've seen that there's a descriptor open on the audio device, but it is also after a recording has been done and we still can access the device. Maybe this descriptor should be closed and then it causes the bug due to a timeout... we haven't been able to figure it out yet.
The OS is Ubuntu 10.10 Server Edition for 64 bits. There is no pulseaudio installed, since there's no X server either. It all goes directly to alsa and when the recordings are succesful we are getting a good audio quality.