I think you might be running into a yIsDown problem on your bone I had an issue with it here: World Translation Of an animation
if you open up your json file and look at the bone in the setup pose skeleton you will see the bone rotation is either -180 or 180 (assuming the rotation of the bone in spine is 0). You need to take the bones initial rotation into account. Spine doesn't tell the full story, some of it data it shows you is different to the actual data.
edit
A Quick way to test this is to (in spine) select parent space, and select the bone in question if the green down arrow is pointing down, the bone is 'flipped' to start with...
you can not alter this, if you move the bone out the hierarchy the 'flip' will move onto the next child bone(s). You also cant change it in the json and import the data.