@tuanphan
I'm having the same issue on my site as well. Custom CSS rules don't apply until I've opened Design > Custom CSS
CSS works properly as long as the Custom CSS section is open.
Only have 1 css rule applied - background image for the header
#header {
background-image: url('/s/[file-name].jpg') !important;
background-size: cover !important;
background-position: center !important;
}