First of all, search engines perceive sites with flash as being "empty spaces." Rather than checking out the content, most search engines just discard the URL. God knows how many people's sites have been rejected because a spider inside a search engine denoted their flash as blank space!
It is also crucial to make sure your HTML is correct. Just because your page is displaying nicely does NOT mean that the code itself doesn't contain errors. Search engines read HTML not what shows up on you pretty pages. The more perfect your HTML code is, the more likely a search engine is to rank it higher. This is why it might be a practical part of an SEO strategy to hire an expert to clean up your code if it is all messed up.