I've never experienced this, Contao is really good with it's SEO, so don't really have a solution for you.
What I find is that usually a bit of patience helps (usually weeks), then you might get crawled by a spider
http://en.wikipedia.org/wiki/Web_crawler
Maybe someone put a 'robots.txt' file into your root?, they block the crawlers and look something like this
Code:
User-agent: *
Disallow: /folder1/
Allow: /folder2/
Also you should look at a Google Webmaster account. Their tag line is "You want to be found on the web. We want to help", does that sound like what you're looking for maybe?
http://www.google.com/webmasters/
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