Honest answer: it's due to the history of both sites.
From what I recall, VgChartz and N4G would join forces as a sales-website. For some reason both sides would then find it better if we'd both go down our own path.
VgChartz since then has enjoyed relative succes and increased media-exposire. N4G kinda lacks that. N4G was also not amused at the way VgChartz presented the numbers (E.G. PS3 at times lower then NPD and nintendo at times higher then NPD, more often then not.)
And as you may have noticed, N4G has a very strong sony-minded undertone to its population.
To delve deeper into this, N4G considers NPD the end-all of all sales-data and generally considers it to be the definitive amount. Unjustified though, because even NPD uses a sample data and doesn't know the entire market. VgChartz estimates a bit differently and as such the numbers differ from time to time (and honestly, uses a smaller sample data.)
So I'd say nothing is wrong and N4G overreacts a little. Their meltdowns during the start of the console war were quite funny though.
The Doctor will see you now
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