My bone axes are not orthogonal

I have a model with a long and rich history. As I was re-rigging it my IK constraint was stretching the bones even though I had “stretch” unchecked in the IK panel. As I was struggling with this, I noticed that the axes of the bones were not orthogonal.
The y axis pointed down the length of the bone in every case, but the x and z axes were not perpendicular and the z at least was stretched.

Here is a screenshot:

legTest2.blend (965 KB)

Look at that highlighted bone! The axes are clearly not perpendicular to each other. I don’t know what I did to bring this situation about, and I can’t find any way to reverse it.

I also haven’t figured out how to recreate this behavior in a new, clean armature.

Any insights would be appreciated.

(P.S. I deleted all the non-relevant parts of the model for clarity.)

Apply the scale and rotation for the armature object (Ctrl+A)

[QUOTE=Richard Marklew;2826975]Apply the scale and rotation for the armature object (Ctrl+A)

I did this (in Object mode) and it worked. Thanks a million!