The transparent primary menu doesn't work if the first section contains the post title module.

Add the following CSS to the first section settings > advanced > main element:

padding-top:0 !important;
Code language: CSS (css)

Alternative: use the full width post title module.

According to Elegant: It works as intended. Top padding of the first section is added via jQuery to make sure that content of regular section is not covered by transparent menu. So settings of the section are overridden.