Finally, I found an explanation to that.
Each DIV inside WP pages seems to be regenerated by the plugin (exact ?). Because of that, the source code of the page (even if there is no D3 integration) is changed.
In my case, a lot of <p> tags are added inside my <div> and generates some gaps.
No worries, I understand that is could be tricky to be compatible with all WP theme (in particular the most adaptive ones).
Hope this help the community !
Regards.
Thomas
Note: I will waiting for a reply post from Ruben before to pass this topic to resolved status