Internet Explorer does not allow the use of file:// protocol URIs within non-File:// delivered pages. This change was made back in 2011 and applies only to INTERNET and RESTRICTED ZONE sites.
See http://blogs.msdn.com/b/ieinternals/archive/2011/08/12/internet-explorer-9.0.2-update-changes-file-protocol-and-cookie-naming.aspx for details.
To workaround this, instead have your extension load the contents of the target script into a BSTR, and use that BSTR to pass into execScript.