I had a problem last week with some customizations via custom.css in IBM Connections 126.96.36.199 CR3. Communities still use the default Layout and colors.
I found that defaultTheme.css rewrites some of my custom.css statements. I had to add the content of custom.css to the end of the xxxTheme.css (lazy but it works), that i have a consistent color and layout change. Tests with @import are not working, because @import must be the first statement of a css file and i need to add the custom.css to the end of the xxxTheme.css.