I may have had the same problem when IIS and QlikView Web Server were running on the same time : In QlikView 9.0, QlikView Server use it own web server ( QlikView Web Server ) to host both Management Console and the AccessPoint (IIS is no more really necessary).
I advise you to check on server if the QlikView Web Server Services is running. If yes, that may be your problem :
If you need IIS to create your own Web site around QlikView, I think you should stop the QlikView Web Server Services and use IIS. If you just need to use the Management consoles and the Accesspoint, you should stop IIS (I mean the QlikView site on IIS if you have other things running on IIS, off course).
If you still have difficulties, please try to add the AccessPoint url in the trusted sites of your Internet Browser
If you need additional info on the QlikView Web Server, please refer to the QVS Reference Manuel Part 1. 4