I think I'm not completely clear on what you're asking, but my understanding is that your headers are not aligning to the leading you have set for it.
One thing that I immediately noticed is that there is no baseline grid being used. In two-column text (page 8), it looks odd having the baselines not match up. I strongly suggest you set this up. By fixing your paragraph styles to the baseline grid, I think your headers will fit as you're wishing them to. (in paragraph styles: INDENTS AND SPACING, choose the drop-down menu ALIGN TO GRID>ALL LINES).
Apologies if i'm answering the wrong question