Upgrading to alsa 1.0.23 fixed it. Link here for the benefit of others:
http://ubuntuforums.org/showthread.php?p=6589810#post6589810
** Changed in: alsa-driver (Ubuntu)
Status: New => Invalid
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[Realtek ALC259] Recording problem - Can hear a lot of noise, no recording
https://bugs.launchpad.net/bugs/640982
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