OK OK...There was a boo boo. I was using this silly function that always got an XML version of the page and never the same HTML that your browser gets. I went with it because it was a smaller download and technically easier to parse (so I assumed it would be faster overall. Problem was, it didn't give you all the links, at least with e621, but wildcritters was fine. So I'm using a different function to get the HTML now, and it's the same stuff your browser gets. It now works as it should, getting every single link on each page it looks at.
Also, I noticed some confusion over what this program actually does. So let me try to break it down a lil better: 1. go to one of these sites: