You have to surround your js with something like this
This works for simple scripts within the field description, like changing some layouts etc. I've not tested this with complexer ones.
For a script within the announcement banner we use this
You will need to use tools like firebug to check if your script is throwing errors . If the script is compatible you might need to add some delay in the script execution. I was facing a similar issue which i got sorted out by using the setTimeout() . I added a delay of 2 sec and the script worked on the popup/modal window
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