It definitely sound like a mastering mistake in the LFE channel. It happens occasionally, but the majority of discs are fine, of course.
And yes, such a problem is independent of the channel count, as long as it contains a LFE that is. If you use stereo downmixing, the 6.1 layout wouldn't matter either way, the LAV downmixer can handle that fine.
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LAV Filters - open source ffmpeg based media splitter and decoders
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