Does google know about non indexed backlinks?

I have around 5000 backlinks built to my site. I do a lot of checking to see which links google has indexed. I index the links manually when I'm ready to and so far 1200 links have been indexed in google by checking using the info:backlink. I always thought that if the link is not indexed it does not count. I checked my webmaster tools to discover that 5300 links are known to google even when the links have not been submitted for indexing? How come?

I found the answer. 1 link was repeated many times throughout 1 site and google counted them all.