Are you saying that sometimes your Windows application icons do not show up on your Mac OS app switcher (and in the dock when launched)? I am having that problem with Quickbooks Desktop for Windows. I keep Quickbooks in my Mac's Dock so while the icon is there, the white dot that is supposed to display below a Dock icon when it is open does not appear. It messes up my workflow and I've taken to keeping Quickbooks in a window that is always visible (even if using a Mac app in the foreground) so that I can just click on it. I prefer things to be maximized (but not "full screen") and to use the Mac OS app switcher. I would appreciate any suggestions to fix this.
Things used to work properly, but something has broken but I cannot tell if the problem started with a Mac OS update, a Windows update, a Parallels update, or a Quickbooks update. That said, I think I have noticed that all of the built-in Windows apps are working properly and that it is the third-party apps like Quickbooks that have this problem.
Kevin, can you isolate which apps have this problem and comment back here? Are you indeed seeing an app ONLY SOMETIMES having the problem or are you experiencing that about half of the apps you use have this problem. The two are very different and could provide a clue leading to solution.