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wont the browser security possibly cause ofther issues..IE..not allowing programs/login pop ups they need to run.
Yes, it can cause problems if you need it for certain web applications. Take !imitation's advice with the scripting, combine that with the trusted zone option. Set only the pages a employee needs to see on the companies website that require scripts. There's gotta be a way to export that and run around with a disk to update, but maybe your admin software will permit that as well.