This is a common little problem I've come across a few times, and the first time it happened it took damn long to find the answer. The main case that I come across this issue is when a have popup jQuery plugins such as thickbox or colorbox which load an image or content in a nice popup. These are generally called via using a class name attribute for example:
This is the standard thickbox one above where a class of "thickbox" is used to call the plugin.
tb_init() is a function in the plugin that initialises thickbox on the elements with that selector. You may need to make your own, or find the function that does it in the plugin you're using. Good luck, hopefully I may have saved you some time.