I reproduces that problem with Smokin'Guns v1.1b2 based on ioQ3 r1725:
When I activates the s_muteWhenMinimized cvar and I minimize the game window during a game, any new in-game sound seems to be played for few milliseconds before being muted. I would expect to have no sound at all and this is what I obtain when SDL backend is enabled.

Here is my sound subsystem initialization under linux x86_64 (Fedora 10 and Fedora 11):
------ Initializing Sound ------
Loading "libopenal.so.1"...
Allocated 96 sources.
OpenAL default capture device is 'ALSA Capture on default'
OpenAL capture device opened.
OpenAL info:
  Vendor:     OpenAL Community
  Version:    1.1 ALSOFT 1.8.466
  Renderer:   OpenAL Soft
  AL Extensions: AL_EXTX_buffer_sub_data AL_EXT_EXPONENT_DISTANCE AL_EXT_FLOAT32 AL_EXT_IMA4 AL_EXT_LINEAR_DISTANCE AL_EXT_MCFORMATS AL_EXT_OFFSET AL_EXTX_source_distance_model AL_LOKI_quadriphonic
  ALC Extensions: ALC_ENUMERATE_ALL_EXT ALC_ENUMERATION_EXT ALC_EXT_CAPTURE ALC_EXT_EFX
  Device:     ALSA Software
Available Devices:
ALSA Software
OSS Software
PortAudio Software
PulseAudio Software
Wave File Writer
Sound initialization successful.
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