Is it possible to download javascript websites that opens in a new window

The website is http://central.mindleaders.com/lms/login.jsp?siteid=eca01

After you logged in, a new window will open with the URL http://central.mindleaders.com/lms/tile.do?def=topFrame

Have you tried follow the login instructions here:
http://www.microsystools.com/products/website-download/help/website-scan-login/

More specificly problably the section:
"Post Form / Session Cookies Website Login : FireFox Live HTTP Headers"

Since A1WD performs login first, you might then just add the new paths into the "addittional start search paths":
http://www.microsystools.com/products/website-download/help/root-aliases-start-paths/