This will occur if you create an icon on your home screen and launch EM-COP from that icon. You get full screen, however if you leave EM-COP to check your email or open another application then try to come back to the same EM-COP session, you will be logged out of the environment.
This happens because your iPad will always force a screen refresh. This behaviour is part of the iPad design and can't be changed.
The only way to avoid this problem is to start Safari and launch EM-COP either by a favourite or by typing the address into the address bar. You won't get full screen, but you will stay logged in.