I have Minecraft pinned on my task bar, but when I click on it, it opens up a completely different cube on my task bar. I have tried re-pinning the other one that opens, with no luck..
Screen cap --> https://i.imgur.com/e48aa.jpg
That would be because the program Minecraft is JAVA based program.
What you're pinning to the taskbar (the minecraft executable from the installation folder) is not the program that's actually used by the game in order to run, what is run is usually the java executable that is handling the program, usually javaw.exe/java.exe/javaws.exe
This java executable is application independant, which means that for every program that you launch that requires Java, a new instance of javaw.exe/java.exe/javaws.exe will be launched and added to your Task Manager.
For example:-
I use a Java based program called PS3 Media Server to stream video content to my PS3.
The program's executable is called PMS.exe.
When I open PMS.exe what is actually launched is an instance of javaw.exe in my task manager.
And so, since Windows refers to this javaw.exe in your task manager as a new and unrelated program, it adds it to your taskbar.
Notice the two green arrow program icons on my taskbar picture, the first one is the PMS.exe that I pinned to the taskbar, and the 2nd one is the javaw.exe process that is handling the program.
So in conclusion, what you've mentioned in your opening post is normal by design.
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