As far as upload, Nikon View NX2 and Nikon Transfer kicks my queue out all the time. I need to start over again and again.
How can this be an issue with the camera? Or are you connecting the camera directly to the PC?
Personally, I have never had an issue with Nikon Transfer on Windows. It has always transferred my images from CF and SC without problems. I have seen a weird problem on the Mac with both CF and SC where the transfer will just stop. Clicking Stop and Start again will transfer the next image and it pauses again. This was happening long before I bought my D7000, though, so it obviously isn't a camera problem.
Just as an experiment you should put your D7000 on a tripod and on Shutter or aperture priority and then shoot images throughout the ISO range of the same subject/ conditions, then compare exposures side by side. I would love to hear an honest assessment of your results.
Interestingly, I did exactly this last week for testing ISO performance. I actually did 3 runs, 2 under available light and 1 inside against a tapestry using the pop-up flash. The resulting exposures were almost identical, except for ISO 25,600 which was slightly brighter.
I wonder if you have a faulty camera.