Make your test check whether the login window is displayed. You can do this using one of the Wait* methods. If the login window is displayed then call a test routine/keyword test that will perform a login and then continue the general test flow.
...
var loginWindow = Sys.Process("Application").WaitWinFormsObject("loginDialog", 3000);
if (loginWindow.Exists) {
doLogin();
}
...
function doLogin()
{
// perform login
}