I found that when I switched to a new proxy Khan Academy wasn't working on most of the computers in my school any more. I don't know why not all since we all use the same one, but anyway, after looking around for ages I finally found a solution. So, this isn't a question, I just want someone to be able to find the answer faster than me.
I tried - https://sites.google.com/a/khanacademy.org/forge/technical/how-to-disable-internet-explorer-compatibility-view and that didn't help me at all. It wasn't listed, and it didn't say it was using compatibility mode. I assumed it was some sort of JS error or something. It wasn't.