Am I losing image quality using Lightroom or Aperture

So, I have been going back and forth on this almost endlessly for over a year now.
I shoot RAW with a D3 and a D3X, for action and studio. But every now and then, I open up one of my RAW files in Nikon ViewNX, oe Capture NX. When I do this and look at definition and sharpness of the image as compared to the same image, viewed in either Aperture or Lightroom, Nikon View wins every time. I notice it most in loose hairs, or distant branches or leaves, The Nikon SW just seems to be sharper and more defined.
I always compare at 100% in each program.
It's driving me nuts! Both Aperture and Lightroom are infinately better to use than the Nikon SW, but, having invested so much in Cameras and lenses to get the highest fidelity, I am reluctant to switch.
I am using the latest version of each application.
PS. when I generate TIFs from the RAWs in the Nikon SW and load them into aperture or lightroom, they do have the same fidelity.
Anyone seen this? is it just a rendering issue on the screen? Will the output look the same? or is it the proprietary RAW files from Nikon that are holding back some critical info that imporved the image?
Would really appreciate your feedback/input
Nick

is it just a rendering issue on the screen?
Yes. In addition to what Sean notes, Lightroom uses a bicubic scaler in its zoomed out views. This means that you get far less moiré artefacts when zoomed out, but will make the image appear less sharp when zoomed out. Capture and ViewNX use a nearest neighbor scaling which appears sharper (but actually isn't) when zoomed out. You should look at 1:1 (100%) to actually compare the programs. Be aware that Nikon applies a LOT of sharpening by default and that the default sharpening in Lightroom is pretty mild. They also by default apply excessive (in my opinion) noise reduction. You can get far higher quality and more detail out of Lightroom than the default rendering in Capture/View but you'll have to work a little on it. The starting points for sharpening are very conservative.
Will the output look the same?
Try it. In my experience, if you work a little, Lightroom is quite a bit better. Once in a while I like the color rendition from Capture NX better (even when using the camera-matching profiles) but those are rare conditions.
is it the proprietary RAW files from Nikon that are holding back some critical info that imporved the image?
No that is a silly myth that Nikon likes to perpetuate. There is no secret info in the file that somehow allows you to get more detail or something. Just try it and you'll see. You can only judge the detail in the rendering at 1:1.

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