Internet Explorer disables Javascript if file is loaded from a local
computer for security reason, you need to click a yellow bar at the top to
enable it. Other than that, I don't see any reason why Javascript may be
disabled.
If you want to stick with web approach developing this application, may I
suggest ZZEE PHPExe:
It is a little bit pricy, but allows you to use all HTML, Javascript,
Flash, PHP, SQLite, etc, yet it creates Windows applications.