Hi Gabriel,
I appreciate your help on this topic, thank you. We had already the suspicion we dont need the WindowID for navigating and are familiar with use of ShortURLs, as far I remember they are stored in a DB table in fact. Certainly as Lucas already mentioned every solution leading to change of enduser behavior is not a possibility. On the other site we cant take any influence on the creating process of favorites through IE.
Regarding that points the only solution seems to find out what the SAP AFP is doing different comparing to our custom framework. I have actually an idea to modify accessing iframe URL to remove this parameter there on load, could work like that:
http://stackoverflow.com/questions/6765356/dynamically-change-onload-for-an-iframe
regards
Edit:
So, I'm not sure I got your point across, but I see you are trying to generate a favorite that would lead one to that page, there is really no need to check the WindowID
and of course: we dont do that in our framework 
. The popup is caused by SAP JS.