This is the same problem that existed before 1.1.9 (From blog: fixed capture problems that came with a recent update for Windows 8.1, affecting users with multiple displays and different scaling
) , but it seems to have reappeared for me. I have two monitors, my Macbook Pro's (Bootcamp with Windows 8.1) at 2880 x 1800, and a second at 1920 x 1080. When capturing from screen region, images are normal if I capture from the external display, but on the main they are enlarged and blurry (see attachments, One Enlarged and one normal).
I recently ran windows update, so there is a possibility a recent update was the cause. I've attached a picture of my update history.