First, I got an error message saying that the operation wasn't successfull.
And the whole thing went bezerrk. None of the pages in JIRA would load.
I had to remove the banner by going in the database.
Has the functionality in banners changed in any way?
I copied and pasted the js into an announcement banner and didn't run into any issues in JIRA 7.2.6 or my Cloud instance. Hopefully you've found a workaround or it started working as expected but if not, I would reproduce the issue and take a look at the atlassian-jira.log. As a test I tried the following and it popped up a window that said hello world with an OK button:
alert( 'Hello, world!' );
If you're still experiencing this issue I would recommend putting in a Support Request to the JIRA team so they can take a look at your instance further as there may be additional customizations that could be causing this behavior.
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