Brianja,
Just curious (if you wouldn't mind sharing) your post-processing workflow? I usually shoot in RAW so my editing is done in Photoshop's RAW editing portion (just before actually loading the image for major changes, i'm sure you know what i'm talking about).
But, back on topic --
Sometimes I accidentally clip the AF/MF switch on my lens and even though they look somewhat in focus on my photos and my AF points light up, the photo isn't actually in focus. Maybe check that? I know it sounds like something too simple but its possible. I can't remember how many times I've done it.
