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Unfortunately what you are seeing today with FF/Chrome/IE 9+ is actually the expected behavior. When you have multiple FOIs from different themes, even if they appear apart from each other, each is rendered into a rectangular PNG image with a transparent background and those image boundaries are probably overlapping. In IE 7 and 8, due to the browser's proprietary way of handling PNG transparency (with the use of an alpha filter plugin) user can actually click through the transparent portion of the top FOI image and the event will reach down to the bottom FOI. But again this 'feature' is available purely due to IE7/8's use of the png transparency filter. Generally speaking this is not supported in other browsers, there are some tricks to implement this (such as the pointer-events mentioned in this thread http://stackoverflow.com/questions/3080746/clicking-through-a-transparent-png), but no widely available solution exist yet.
Maybe try letting user control the display z-order of the themes so that the active (clickable) theme is always on top?
Thanks for the reply. I will have to let them move themes up and down in order then.