Guessing it's to do with the size of the viewfinder, bit like looking through pinholes sharpens things up. Daresay there is an optical explanation for it and along the same lines of how the image always looks better on the LCD than it does on a monitor.
To prove the theory, does it look good through the viewfinder, not quite as good on the LCD and worse on a monitor.
The 100mm would look better because it's a sharper lens, but don't think its a defect or a micro adjust focus problem.
One of my eyes is weaker than the other and I have to make sure I use the better eye to check my photos otherwise they can look less sharp than I expected even with glasses on. Make sure the viewfinder diopter is adjusted properly, turn the little wheel until the focus points appear at their sharpest.