Check the anchor point and position values for decimal places.  If the screen capture wasn’t full-screen size then the resolution could be an odd number.  When dropped into a comp After Effects will set the anchor and position values to half the res, which if it’s an odd number will give you .5 values.  This will cause more softness when viewed at half-res and is generally something you want to avoid.
I've run into a bit of an issue which I can't seem to resolve. I've imported some screen capture footage into AE. The footage is very, very crisp but dropping it into a comp softens it ever so slightly, despite having the quality set to bicubic. Any thoughts as to what might be going on here?