It's not intended to be an aid, just an aiming line. Normal behavior would be like in the picture below. As soon as the shot loads the aimer is already on top of the flag. If you are hitting off the tee it should be in the center of the fairway.
I've seen some occasions where the aimer did not match up exactly where it's supposed to, but those situations are usually few and far between, not an every hole thing as you mentioned. When was the last time you cleared your browser & flash caches by chance?