I only shoot RAW. I'm using Lightroom 4. I used a tripod. You bring up a good question though. I don't think I'm using any sharpening automatically. Since we have no idea how the image is really being captured--until it opens in a converter--then that may be the problem.
However, I'm not a real fan of using sharpening on anything but originally captured sharp images, and then only on the finished product--in other words, if I don't have a sharp images to stat with, it gets deleted. (Unless I'm using it for web use only and you can't see the softness.)
I can tell easily when images start out soft and have been artificially sharpened to "look" sharp. Not so much with smaller prints or smaller web use, but at larger sizes, it's quite evident--and I really despise that look.
The reason I posed this question is that using my 70-200L (with IS turned off) for some infrastructure images, I noticed that even at the sweet spot, I was seeing a blurry image. It didn't look like lens blur, rather, it looked like resolution problems, where the image is just not sharp, but fuzzy looking. Something like when you see the distant background edges at full resolution on a landscape image, where you have diffraction and haze in the air.
But I'm seeing this even on images that are 25' from me.
So I went back and looked at some recent images I did with portraits using the same lens, while hand holding it, and at 100% the focal point was razor sharp (usually the eyes).
I set up a ruler and shot the middle and after the second shot suddenly remembered that I had recently enabled ISO Noise Reduction in my camera. So I turned it off and shot a few more images. The image with noise reduction enabled was, to me eyes, softer than the image with NR disabled. In fact, the softness looked exactly like it did on the other images I had shot of the infrastructure. However, it was worse on the infrastructure do to the distance of the object.