Same problem here on a System76 laptop, have been talking to them but they haven't been able to recreate it yet. Likewise, disabling auto-mute fixes the problem until reboot under Ubuntu, luckily I also have an Arch Linux dual boot which I just haven't rebooted since toggling auto-mute. The below information is from Arch:
tapio@tartufo> lspci| grep Audio 00:1b.0 Audio device: Intel Corporation 6 Series/C200 Series Chipset Family High Definition Audio Controller (rev 05) 01:00.1 Audio device: NVIDIA Corporation GF116 High Definition Audio Controller (rev a1) hexdump /proc/bus/pci/00/1b.0 # attached uname -a Linux tartufo 3.4.8-1-ARCH #1 SMP PREEMPT Thu Aug 9 21:21:22 CEST 2012 x86_64 GNU/Linux If there is any other information I can provide, please let me know. I'd appreciate it if someone could compare their stuttering pci config with mine, similar to in this thread https://bbs.archlinux.org/viewtopic.php?id=129990 ** Attachment added: "Hexdump of PCI config" https://bugs.launchpad.net/ubuntu/+source/pulseaudio/+bug/1019693/+attachment/3269685/+files/workingPCIConfig -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1019693 Title: [HDA-Intel - HDA Intel, playback] Audio stuttering To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/pulseaudio/+bug/1019693/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs