I have 'Check for externally modified files' turned on and generally that works for me, but I've found I can trick PhpED by doing the following:
Open a file both in PhpED and a separate text editor
Change the file in the text editor and save
Click back to PhpED it detects the change and refreshes
Quickly go back to the editor, make another change and save, then click back to PhpED
PhpED does not always detect that new change even if I click out of and back into PhpED multiple times
Using a test file located on a remote Windows system (file share) it failed pretty much every time. Using a local file (desktop) it took a few goes to make it fail.
I think in a normal editing/editing scenario with reasonable delays between each save works, but it does look like the file change tracking is not quite correct.
On the other hand, if you never get a file change notification, maybe double-check the setting for checking externally modified files is enabled. You might need to report it direct to NuSphere.