Changing a div's height by code introduces a "ghost" padding I can't get rid of

I have a div whose height I set as equal to that of its parent at window load and resize.
After I do this, a ghost padding appears, Chrome inspector shows it colored as padding although it's supposedly 0.
jQuery's css("padding") returns 0px, height(), innerHeight() and outerHeight() all return the same height.

So, what may be happening here?
How could I fix it and remove the padding?