I had raised this issue to the support by sending them email. Trying my luck by posting the issue here. Had 2x Application Server version 3.3, upgraded to 4 and the seamless windows does not work. It used to work with the older version. Interestingly enough I see TWO toolbars at the bottom of the screen, one for my desktop and one for the remote desktop. PLEASE HELP.
What are you publishing?? In the new version you can publish desktops too, make sure you are not publishing a whole desktop. Did you upgrade the client too??? Nixu