I can confirm the bug and the workaround with the following soundchip:
00:14.2 Audio device [0403]: ATI Technologies Inc SBx00 Azalia (Intel HDA)
[1002:4383]
Subsystem: ASUSTeK Computer Inc. Device [1043:82bb]
Kernel driver in use: HDA Intel
Kernel modules: snd-hda-intel
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pc speaker makes loud pops, apparently before and after sounds are played
https://bugs.launchpad.net/bugs/444960
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