Hi Ian,
Sometimes that will happen and may depend on the file size of your SWF file. Normally it is a quick flicker before the Flash loads. In any case the alternative is to skip the SWFObject and surround your Flash file with text and links in the HTML to help with
SEO. Additionally, I believe Flash 8 and later versions allow you to add XMP Meta data, which might add some potential lift. Hope this helps.