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My 5.1 surround sound seems to work just fine except anything I plug in to the line in jack of my sound card only comes out of the the front two speakers and the sub woofer.

Is there a setting in PulseAudio or Alsamixer that I'm missing?

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I'm not entirely sure but I think it may have to do with the fact the line in jack on your sound card is not compatible with the surround sound type systems meant for TVs. I had a 5.1 surround sound system once that I used with my computer and it was most definitely not surround sound, it was like stereo, because it was just a stereo jack on my sound card. – xjonquilx May 18 '12 at 2:52

Yes i agree with xjonquilx.

your line in is most likely stereo which is different than 5.1, because stereo is analogue and 5.1 is digital. But it is odd that your sub would work when your playing stereo.

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