Since installing Windows 8.1, I have been experiencing issues with script loading in IE 11: When the server responds with "304 Not Modified" in response to a script request, bad things happen. Specifically, I encounter script errors that would normally be caused by a missing script reference or having references in the wrong order (e.g. "Unable to get property 'foo' of undefined or null reference"). Doing a force-refresh (i.e. Ctrl+F5) corrects the issue until the next page load.
Based on what I see in the IE 11 developer tools, it looks like the scripts are loaded correctly. I can open them in the Debugger view and the content appears to be correct. Perhaps IE is just not loading them in the correct order in this scenario?
I noticed this problem myself and then someone else (who has also recently installed Windows 8.1) informed me that it appears he is experiencing exactly the same issue on a different site.