I'm confused when you say:
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playing the file should sound identically whether I'm playing through my stereo output or outputting it directly to the subwoofer
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If you're wired correctly you should ALWAYS be playing through the sub since it handles the bass management.
Can you specify exactly how you have things hooked up?
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I just re-read your original post. What do you mean by:
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I do have output from the sub in stereo operation. It's just significantly lower.
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As well as:
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If I play content that is to be reproduced only via the subwoofer (i.e. a sound containing no information over 85Hz), it will sound substantially louder if I output it directly to the subwoofer compared to just playing it "in stereo" and letting the bass management redirect the signal.
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It sounds like you have a feed going to the LFE input as well. Unless you're actually mixing with a separate LFE channel, there shouldn't be anything in that input on the sub. Also note that the LFE channel probably has the +10dB switch active, which is correct for a room doing Dolby specific encoding. This boosts anything on the LFE input by that much!! Is this what you're doing and hearing?
More info, please.