I'm assuming you are running the latest version of View NX2.
You mentioned converting from NEF to JPEG. Does it render NEF's appropriately? If so, what steps did you use for conversion? It's possible the conversion created a bad JPEG - but not likely unless it was interrupted. I normally just select the NEF images to be converted and use the Batch function in View NX2. Even better - try converting a single image at a time.
If the NEF's are not rendering properly, it's likely something they are corrupted. The most likely errors are either corruption during import or a faulty card. We see a lot of reports of bad SD and CF cards. There are a few reports of problems with good cards. There is not much you can do with a bad card. You can try a variety of Rescue and Recovery programs. The basic thought is only buy cards from a reliable dealer - and don't look for bargains that are too cheap.
If you have good files, you should be able to view them accurately. It's possible to create green tones through an imporper setting of White Balance and Tint - but you would have to really mess up your settings to do that. If so, you should be able to go into View NX2 and select an Auto WB and a Standard Picture Control setting and render a good image. If that works, the issue is simply bad camera settings and all can be fixed.
If the software is unresponsive, be sure you have enough RAM and are processing a single image at a time. Process the image, save it, and then convert it to a JPEG. Some steps can be memory intensive - I've found Straighten is sometimes a problem.
One more thing. Is the camera working properly and do you have the same problme with fresh images? My concern is a bad SD card and it woudl be great if you could test the camerea and software with a card that is known to be good.