For sure the boom height difference might have affected how the board felt.
But just to throw a curve ball in this, on my wave boards, I actually put the boom a cm or to higher in choppy or super windy weather. On such a board in such conditions, you will bounce around a bit anyway, and with the boom higher the board runs a bit more free which will make the hit it takes up front not transfer as much to the rest of the kit. In smoother waters, I use a lower boom since it enables a better body position int he wave riding.
But for you: yes, try the boom a bit higher.