Do you mean an external file (<script src="file.js"></script>) is not updating when you use Ctrl+Shift+r? It definitely should update. If your cache isn't behaving normally, you might clear the whole thing and see whether that improves the situation.

See: How to clear the Firefox cache

If you have a large hard drive, this might take a few minutes. If you do not see the number going down on the page, you can reload it using Ctrl+r to check progress.

In extreme cases of brokenness, you may need to clear the cache2 folder physically (while Firefox is closed). It is in the Local AppData path:

C:\Users\username\AppData\Local\Mozilla\Firefox\Profiles\123.abc\cache2

Hmm, normally, I would verify file retrieval using the Network Monitor section of the Developer Tools. I'm not sure how to check without opening the developer tools. Are you using the about:cache page, or just finding the script to be incomplete/incorrect compared with what you last saved?

I cleared the cache manually, and though it would work to refresh the page once, it wouldn't refresh properly after. Watching the network, the javascript page didn't get called until I clicked a button. I then cleared the network console and suddenly, ctrl+f5 started refreshing properly again. (I also updated the javascript page for the main page once and hard refreshed, which could have caused it to work again). I don't exactly know why, but problem solved! Thanks for the help.