Sharepoint - JS files returning Cached (Old) Versions Despite Update
Discovered the answer to my own question. If Script (or CSS) files are kept in normal libraries they will get cached internally to SP and only rarely updated. However if these are files are maintained in the "Style Library" (a built in library created by SP) they will NOT be cached and will update normally.
It's easy enough, once this known, to create your own set of folders within the Style Library and manage your scripts from there.
Most probably it's an issue of the file getting stuck in one of the server's caches.
Is the BLOB caching enabled on the server? If yes, you can try clearing it.
Are Publishing Features enabled on the server? If yes, make sure that you have reset the Page Output Cache and the Object Cache also.