UPDATE
I have reverted back to Jquery 1.3.2 and everything is working, not sure what the problem is/was as I have not changed anything else apart of t
Ok, I finally found my solution.
If you are using templates on your view (using Moustache.js, or others...), you must take into account that some of your classes can be loaded twice, or will be created later. So, you must apply this function $(".datepicker" ).datepicker();
once the instance has been created.