As usual I'm replying to my own post.

I've figured out that it's when I group the ikHandles of each branch that this happens. When I first create 1 ikHandle per branch sharing the root node then both ikHandles affect it ok. The problem is I have another ikHandle on each branch. I make two groups of ikHandles, 1 per branch. This yields the right effect, but it only works with the right side of the branch (no matter which order I group them together). This is really weird. I can't figure it out.