Fixed header – Site title and menu problem not aligned when scrolling down

I use the matrix theme.
I have changed the logo top spacing to have the site title aligned with the menu bar.
But there is something strange when I scroll down.
First the site title is not aligned anymore and it looks like it is in a grey banner.
Second, when you scroll to the top of the page, the top spacing doesn’t exist anymore and the title is not aligned again…
I don’t know if I’m clear but I would like to have the title and the menu bar always fixed and aligned…

Thank you !