Many CSS of the header and LOGO will be reset by javascript (in jquery.samsara.js) when you scroll down the page. The other hand, when you changed the orignal CSS for desktop, you must change the responsive CSS for the mobile version with CSS media query at the same time.
I don’t know how you changed the CSS, but generally speaking, the problem which is caused by user custom code is not included in the support.
Anyway, I would like to know your website link and hope I can help you to analyze your custom CSS, and give you a general solution.
Thanks