Masthead & TLN Shifts up in Portal AJAX Framework Page

Hi Experts

We have integrated fiori, webdynpro java/abap applications to a Portal 7.4 system. The Portal has been customized with a custom Masthead ( modified) and a Hover TLN. The issue with when ever we open up any WebDynpro JAVA/ABAP application, the whole portal shifts up and the masthead and TLN gets hidden. They are still present but the screen just moves up. The Fiori and UI5 apps just work fine. And then issue is available only in Chrome, works fine in IE.

Here are some screenshots

1) Portal when running any Fiori/ui5 apps

2) When clicking on any Webdynpro/java app

As you see, the whole screen moves up and hides the masthead/tln

I am not sure what could be causing this issue.

Any help/pointers are much appreciated.

Thanks

Sandip