I've found a bug related to the integration with the Taskbar. What's happening is that clicking on a taskbar item is creating a second instance of the application rather than bringing interacting with the existing application.
More specifically, I have this happening with Outlook and I believe it may be related to multi-monitors and grouped application windows. I can reproduce the problem. It does not happen when I turn off "enhance the taskbar".
Steps to reproduce:
1) Have Outlook running on monitor 1
2) Have a second window up (e.g. reminders, new email, etc). running on monitor 1
3) Minimize the applications and have the focus on other window
4) Click the icon in the toolbar. Most often it will show you existing windows. Sometimes it will launch another Outlook instance.
5) Repeat this test, but first open another popup on monitor 2. In this case, I've gone ahead and opened a "new email" on monitor 2.
6) Because of my multi-monitor setting, the icon for this new windows is only on monitor 2.
7) Click on the taskbar icon of Outlook on monitor 1. A new instance of Outlook will launch on monitor 2
At this point there is a disconnect between the task bar and the app.
8) Close both the new instance and the popup window on monitor 2.. This brings you back to your original setup. However, since the two seem to be out of sync, click the application icon in the taskbar on monitor 1. It will open a new instance of Outlook on monitor 1.. Same problem, just showing that it's following the multimonitor. This will continue to happen. If you close each new instance, clicking the original taskbar item will launch a new one. If you leave the "secondary", repeatedly clicking the application icon will not create a new one. It's "sort" of synced to one of them.
9) You can "resync" them by explicitly hovering over the icon and choosing the selected primary application.
10) if you do that then a) a new instance won't be launched they will be back in sync and you can minimize and click on the taskbar icon without a new one being created.