I'm having a problem where I am editing an external javascript file in PHPEd, saving it, and then running the debugger and finding out that the changes to my external javascript file are not updated in the debug session. I assume this is because it is using the cached version of the file. Usually I press Ctrl+F5 to remedy this, but that doesn't work in PHPEd for obvious reasons. Is there a way to disable caching of external javascript files and make it so the internal Chrome browser will always load the most recent version of external files in a debug session? Or is this caused by something else?

What web server do you use?
Is it apache?
If it is apache, you have to check cache options. Some say "smart" developers add expiration header and this is what triggers caching in browser. This is often fine for production where you don't alter scripts, but it's definitely not good for the servers used in development.
Perhaps, you may want to turn mod_expire off completely
see http://httpd.apache.org/docs/2.2/mod/mod_expires.html for further details