Hi @computerpraxis,
I believe you have identified the cause of this problem in your other post, Same AUI.dialog2 appears 2 times in Page Source. If your initialisation code is trying to find the dialog by ID, and there are multiple elements with the same ID on the page, you will always receive the first one in DOM element order.
I suspect this initialisation problem will go away once the multiple dialog issue is also resolved. Check the other post for more details on how to do that.
Cheers,
Daz