I updated to Fusion 8.1.0 while still using Yosemite (OS X 10.10) and immediately noticed an issue where windows for Windows applications would take focus when the cursor moved over them or a Windows application was performing a background operation without user interaction despite the fact that I was working in an OS X application. At the time there were other screen rendering issues and everything seemed to be resolved once I upgraded to El Capitan (OS X 10.11), as that upgrade had several enhancements for iMacs with retina displays.
Well today, in particular, I noticed that the window focus problem was back in full swing. I was working in OmniGraffle and every time I navigated my cursor over to the Color palette, the Microsoft Word window behind the Color palette would take focus and all other Windows windows would also come to the foreground ahead of any OS X windows that were in front of them. Also, anytime an e-mail popup occurs from Outlook, all of the Windows application windows come to the foreground despite the fact that I am working in an OS X window. I use Unit mode because of my workflow—I need to be able to switch between Mac and Windows applications seamlessly just as if I were working in a single OS—and this bug is disrupting my workflow.
Has anyone else come across this problem?