Question: Why is it that when I do a standard Google search for my website I get well over 4500 links that show up, but when I do a "link:" search, I only get 3?
"Link" means the back links you get indexed by Google.This tool is now not so accurate.Try Yahoo or Google's Webmaster tool. And when you search for your site,the result shows how mnay pages in your site are currently indexed by Goolge. So you can see the difference?
Google backlinks don't update soon, use Google Webmaster Tools, it will show you the accurate number of Google backlinks
in reality google will have checked through all of your backlinks but it only displays a certian number in the link: tool, I don't know why, but rest assured all of your links would have been crawled