[eluser]slowgary[/eluser]
It's hard for me to imagine your scenario. You have pagination links, whereupon clicking one the user should be taken to that given page, but any given page will ALWAYS have a set of JavaScripted tabs where the second tab needs to be active?
Maybe there's a better way, but I'll wait to see if you can clarify my above mentioned confusion before I spend any brain cycles on something.
I'm sure you could just store the markup returned by the call to $this->pagination->create_links(), then traverse it and add your #anchor using a str_replace or regex or something, but it seems like a bad solution.