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.