I've had zero problems deploying the BLU-107 in both Auto and CDIP. The one thing that made all the difference for me was changing the BOT (Bomb on Target) Option, This is found in the top right of the AG armament page after you've set up the ripple of the BLU-107.
What this does is change the point in the ripple that the HUD symbology is targeting for, by default it set to CTR which means the jet is trying to give you release info for the center of the string of bombs. This causes many problems with bombs that have a very short fall time, like the BLU-107 or any of the retarded bombs. Changing this setting to 1, which means the jet is giving you aiming symbology for the first bomb in the string makes everything much more predictable. I've had no issues since changing this setting. Of course if you're using Auto mode you should place the target point at the beginning of the runway, not the center.