After starting with a stock armature with a run cycle I added a few of my own bones for various armor pieces on my model. As the stock model is too large for my game and the engine requires me to apply the correct scale before export I scaled the armature down (my mesh is a child of it). After applying the new scale and viewing my run cycle the bones from the stock armature I built on top of are fine, where my new bones explode out to new positions in all directions. It feels to me like the individual origins of my new bones are offset somehow, obviously I have missed a crucial step when adding them, what was this step, and how can this problem be fixed?
After applying scale: