Crackling in the downmix is usually due to clipping. I also wonder if there's a way to see if there's an included downmix coefficient table on the disc, or even to customise the table manually within the table - that would be a great feature for Beta 2 (hint hint :P)!
The other problem with downmixes is some tracks might have out-of-phase elements (usually vocals) but there's nothing you can do about that. On the DVD-A I ripped there's about 3 of 26 tracks that feature a noticable out of phase vocal.
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