Hi Monica,
This is very simple.. from your own answer you can understand the issue.
The application runs in standards mode but you are trying to open it in quirks mode.
If you want it to open in portal content area you must use a standards mode framework like AFP Standards.
Another possibility is to make the application run in quirks mode --> in the iView itself add the following in application parameter sap-ie=EmulateIE8
BR,
Saar