Chris
Have you checked what level of security you've got set for the internet? (Go to Tools, Options, Security tab). If you click on the "custom level" button, you shoud be able to "enable" all sorts of stuff. There's a "scripting" section where you can enable Java script.
If this isn't the problem, have you been to Windows Update recently - there might be a patch for IE which might reset the option and / or re-install the JavaScript processor.
Cheers
Ben