I think it's down to the sample base, and how new samples are manipulated as old ones are replaced, and how the recent huge increase in sound editing parameters cannot easily be reconciled exactly with the older editing menus with less functions.
A really good example was my mp3 demo of Chariots of Fire. This was great on the 3000, but everything was wrong on the 6000, maybe the worst example I came across, due to the many sound edits. That's the very reason I chose it as a demo of 6000 sound substitution and editing example. If you had the original technote disk you could see the difference and what could be done. Technote later released the disk in 5000 format, and that was better on the 6k, but I still preferred more tweaking. Lots of other tracks have been fine, so it is a bit of pot luck.
I think realistically there is a limit in what they can achieve in backwards compatability, because otherwise it stops you going forwards with improvements. That's why I advise re-saving on each new machine rather than jumping generations, as a broad generalisation, it tends to give better results overall in my experience, but cannot be perfect.
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