You are attaching via USB either way...unless there is a USB version difference between your camera's cable and your card reader's cable (or the port you are plugging into), I don't see how there could be any real difference other than the fact that you are dealing with larger files which can certainly happen as you upgrade to a new body.  

The difference could be the new software (no choice here) processes the image more slowly as that is the other change made at the same time. I would think the build in reader would be faster than the USB but maybe not. At any rate it is what it is. 

Thanks for that. I've been away for a bit so a bit slow here. I have been using my built in card reader in the computer. I realized after a bit the files are likely 50% bigger but it is easily twice as slow even using the reader as opposed to cable as I always did before. I just have to leave it churn away when there's a lot I guess. I look into the photo mechanic. Thanks again.

I've had a d7000 for a few years and started out using NX2 to edit and convert RAW (NEF) to jpg. That was fine for a while but I wanted to add watermarks mostly and went to Corel paintshop Pro to avoid the ongoing fees of PS. That was a bit better and fine as well although a bit cumbersome really. I just upgraded (yesterday) to a D7200 and took it out to try some shots and see what it could do. To my horror the shots looked awful in Paintshop x7. They were washed out and flat with a red tinge and not crisp at all either, like looking at them through a hazy pink filter or something. I shot jpg as well so loaded those from the card direct. They were fine. I also found the NEF files looked fine in NX2 BUT I could not edit them. Even cropping just got me a blank screen and 'unsupported file type' message. Nikon's file in Nikon's program?!

Ok writing this I had a thought. What about transferring straight from the card/reader instead of patch cable from the camera as I always did with the 7000. Tried that and they looked fine. Problem with this is navigating to the folder I want to save them too becomes a bit more arduous. The other thing is doing the same with NX2 still tells me unsupported file type even directly off the card. 

Can anyone shed some light for me. I read somewhere of an inability to transfer files with a cable. I'm guessing that is only NEF files. Oddly the card transfers seem slower than the cable transfers even with the d7000 (I did 500 the other day so tried the card). Not just slow for a huge batch but each image was taking quite a while then I was used to with patch cable. Can anyone shed some light. BTW my NX2 is the latest version available. Thanks.