I have exactly the same problem, interesting that we both have this request today.
Here is more information: I have a product built using CodeIgniter. I want to start using Jquery Mobile to make a mobile version. Controllers are executed as "base_url()/controllername/function" -- so I would 'execute' something like "localhost/messages/list1" to list messages, Then CodeIgniter does it's magic to turn localhost/index.php into executing the correct messages.php in the controllers directory and choosing the list1 function. (I hope I explained this ok). I just today loaded up jQuery Mobile to get started, and if I make an href like this: <a href="http://localhost/messages/list1">Messages</a> -- which works nicely from the browser, of course it does not work, since jQuery Mobile rewrites the url to go to
http://localhost/#http://localhost/messages/list1. If I change the href to point to index.php --- <a href="index.php">Message</a>, then that works, but is not what I want, which is messages.php, executing function list1. (But I see the navigation) I could also put in rel=external, that does 'work,' but then I get no hash navigation, which is bad. I could set some CodeIgniter flags to read url's differently, but that would mean rewriting a lot of the application, which depends on the a/b/c method of url passing, not the a?b&c method.
I am sure there is a way to get around this problem, maybe someone else knows how to do it. I hope you can help.
thanks in advance, I am very psyched to use jQuery mobile, I use jQuery and love it!
Mark