Some taskbar pinned icons are duplicated when an instance of the application is running

Two possible reasons and a solution...

Reason 1

I believe it something about do with the program not taking advantage of Windows 7 features (or APIs). Since this may be the case, Windows thinks it is two different programs. You will have to wait until VMware Player updates its software to take advantage of this new feature. This is the same problem I once had with Google Chrome. After a Google Chrome update, it was resolved.

Reason 2

Another reason, you could have pinned the shortcut of the file instead of the actual program. Find actual program, then right click it and select Pin to taskbar.

Temporary Solution

If the first reason is the case then here is a temporary solution. Open up the program, so that you have duplicate icons. Then right click the duplicate icon (the new one) and click Pin this program to taskbar. Next, right click the original and select Unpin this program from taskbar.

Had this issue with Eclipse Mars 64 bits on Windows 10 Pro x64 Insider Preview Build 10130. The only way I managed to fix that is by executing Eclipse as it was a Windows Vista app:

  1. Remove any pinned icon to fom the taskbar

  2. Right click on the Eclipse executable -> Properties -> Compatibility tab -> Compatibility Mode

  3. Check Run this program in compatibility mode for

  4. Select Windows Vista (any of them).

  5. Execute Eclipse by clicking on the executable and pin it when it's fully loaded.

I didn't need to add the -vm flag in neither the shortcut (C:\Users\[Your User]\AppData\Roaming\Microsoft\Internet Explorer\Quick Launch\User Pinned\TaskBar) or the eclipse.ini file. solved it for me:

Taskbar icons get duplicated when a shortcut is pinned to the taskbar, rather than the program itself. The solution is to find and remove the extra shortcut. The most straightforward way to do this is simply to right click and “Unpin” all the icons for the program in question, launch the program via the Start Menu, and then right click the running program on the taskbar to re-pin it.

Sometimes we’ve run into situations where this doesn’t resolve the problem. There’s usually a hidden shortcut that is being referenced by the running program. In this case, the solution is to “Show Hidden Files” in Windows Explorer, and navigate to the system path for taskbar shortcuts. This path is : %APPDATA%\Microsoft\Internet Explorer\Quick Launch\User Pinned\TaskBar – there you can attempt deleting the shortcut manually, and re-adding it once again.