This is the 'flash of unstyled content' bug, often abbreviated 'fouc'. The browser is starting to render the page before it's loaded all the CSS assets. You need to include your CSS in the <head> tag using a <link> tag.
If it's still happening and you don't want to track it down, you can hack around it by changing your body tag to say <body style="background-color: #000">.
But sites with black backgrounds are getting less and less popular because they're harder to read and lots of audiences (older people, women) find them off-putting, which may or may not be OK depending on your theme.
