Are you talking about the settings in the player? As far as I know, the only time that the player would actually use those speaker settings would be when decoding and then outputting as multichannel PCM via HDMI. When the player decodes DD+ and TrueHD content, it re-encodes as high bitrate Dolby Digital (the HD-A2 uses DTS, but the A3 changed to DD) and I don't believe that it does any signal processing between the decode and the re-encode. If I'm right about that, the settings are disregarded entirely.
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gonk
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