Okay... I wish I could explain what's going on here a little better. It's not exactly clear.
Target bones are very new. They can have some "interesting" behaviors when associated with smart bones that haven't been completely figured out and resolved.
What happens deals with the rotation of a bone that is pointing to a target when the target is "pulled up" past the "end" of the aiming bone. This can cause a sudden "flip" in the rotation. An extreme negative or positive value in the rotation that isn't visible because it's the "same" rotation but sort of opposite. When a smart bone is added to this it can completely break that smart bones key frames when the bone rotates like this. A way to avoid this is to never move the target bone "below" or less than the length of the aimed bone. This doesn't work well, because the target bone movement is linear. You still get pops.
I have a new, really awesome rig using target bones that I've been working on for a couple of weeks and made some interesting discoveries that might help with smart bones and target bone issues like this.
One cool trick I found... don't put the smart bone action on the actual bone that is being rotated and scaled by a target. That is where all the trouble starts. For some reason the bone manipulated by a target behaves in odd ways.
I use an extra bone that is a parent of the aimed bone in the setup. In this case it would be another bone that is the parent of the shin or calf bone. The shin or calf bone would be set to "0 0" position. It's has the same origin.
Then I set the
Angle constraints of the shin/calf bone to "0 0" in the bone properties drop down. This forces that new extra parent bone to rotate instead of the actual shin/calf bone. For some reason the "flip" doesn't happen on the new this extra parent bone. It sort of stops the bad behavior. Like a teacher in detention or a security guard at the mall

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This "extra" bone would then have the smart bone actions to move points instead of the ACTUAL shin/calf bone. You don't have any rotation of the actual bone since it's Angle constraints are now 0. Only the new parent bone rotates because it is being "pushed" around by the child bone that is aiming at the target. They both have the same origin so it works like a regular target bone set up.
I've found that using extra bones in the hierarchy can overcome many of these issues. The trouble is... it's really hard to describe. I've tried to do a video tutorial several times and it just feels more complicated than it is. The tricky part is keeping track of the parenting.
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My new rig is freaking off the hook. Will be posting download and tutorials in the next few days.
It allows for complete and total control of all the joints independently. Instead of a target bone "chain" that moves all the connected bones, you can control each part separately. Drag the hand target and only the forearm rotates. Drag the elbow target and the bicep and elbow move but not the hand. Rotate the bicep and the whole arm rotates. You can drag a target bone for "scaling" or "foreshortening" perspective of limbs, or ROTATE the target bone to get "circular" movement instead of "linear". Plus, all of the smart bones work perfectly without issues or popping with the "standard" smart bone/target bone set ups.
I love this rig!!!!!!!! It has everything I ever wanted in a rig and is so easy to pose characters. I can "rotate" the entire arm or leg in a "circle" (like when throwing a ball, or a walk cycle), then I can key the target bone to create "foreshortening" of the limbs for perspective. The trouble with target bones was that it only allows a "straight" linear motion. I needed to add in a parent structure that allows for "rotation" movement of the target bones. Another feature is independent joint targets. I can smoothly animate the location of the elbow/knee with no pops. I also figured out how to add in IK "squash" to limbs. Target bones only have IK stretching by default. This trick breaks IK squash and stretch a bit though. Still working on that issue.
Sorry for rambling... I keep seeing all these issues with target bones and smart bones and really need to get this info out there ASAP.
