My nutrition shop websites for tampa and brandon were coming up on page one of google search results and now they have dissappeared. The 2 websites serve different markets although they are close geographically and have the same products, keywords, and layouts. Brandon, FL is considered a suburb of Tampa, FL and could be grouped into the Tampa Bay area. There's also a mirror site nutrition shop setup for orlando. Is the google search ranking drop because:

1) from a flash banner recently added on the front page

2) is the site just being re-indexed on all search engines b/c of new content?

3) is it seen as duplicate content as there are separate websites for the cities of Tampa and Brandon but with the same content?

What can be done to fix this? Thanks!