Think I've found the answer and it does seem to be the preview, This may be worth a read for any Lightroom & Nikon noobs like me.
The issue with the Darker images is Active D lighting, the preview stored with the RAW is the image taken with ADL and the only RAW converters that recognise ADL are the Nikon ones. Apparently the way ADL works is the photo is taken a few points of a stop darker than what is set and a marker is contained in the NEF file to tell he Nikon Raw converter to apply the ADL algorithm, Lightroom does not support this
so shooting RAW with ADL is pointless unless you use Nikon Capture NX. Another way to get rid of the sudden change is to switch your render preview from the default Minimal to Standard, the Standard preview is taken from the RAW itself but may take a little longer to show.
The issue with the red football kit seems to be another Lightroom downside in comparison to Capture NX2 but apparently it's much better in Lightroom 3 and can be sorted by switching Camera Profiles from Adobe Standard to Camera Standard, I've tried it and it makes a world of difference especially with harsh saturated reds that seem quite common in Lightroom.
This guy
http://ishootshows.com/2010/01/22/lightroom-3-vs-nikon-capture-nx-2/ has gone into quite a bit of detail about the differences between Lightroom and Capture NX, very subtle but depending on what you shoot it could make a world of difference
Hope it helps somebody.
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"I'm playing all the right notes but not necessarily in the right order" - Eric Morecambe
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D7000 and too many lenses.
