That's a new one to me. I can't quite make out any of the text on the taskbar button that keeps appearing, but that icon reminded me of the old TOR application. However, that would be an odd thing on a business network, so I'm sure it's not that. Are you able to capture what it is that is popping in and out?
So you're using Chrome to access the Citrix portal, and from there launching the Windows desktop version of the GUI. Did I understand that correctly? What is the patch level of the GUI?
--Matt