Hi Eida,
I suspect it could be one of the following:
1. Work protect mode is configured to open in a new window.
Try changing the work protect settings according to documentation:
WorkProtect Feature - Portal - SAP Library
2. The iViews that are opened are now configured to open in a new window.
To check this go to the iView properties and search for the "Launch in a new window"
property and make sure it is with value "Display in portal content area". It should open the iView in place.
Best regards,
Etay