You configured a customized homepage for IE by GPO.While the homepage configured by GPO is applied OK in IE8, the same in IE9 isn’t working. However, after you run gpupdate /force, it works.
It happens only when you create a new user profile
By default branding is kicking in, it will lead to homepage GPO not working.
You can disable branding by configuring the following policy: http://gpsearch.azurewebsites.net/Default.aspx?PolicyID=561