With a number of windows open on the Desktop, clicking any application Taskbar icon may not always minimise that window.
Nothing wrong with your system. It 'may be' a bug in Windows, and if so it is unlikely to get fixed. Another possibility would be a coding error in the application. My guess is that Microsoft expects certain features to be encoded in all Windows applications, eg File/Edit/View menus and so on, and if the "Taskbar minimise" is one of those expected options, it may not be well coded in the 3rd party application.
However, I have noticed this with Windows' own native applications so I always put this down to a "Windows thing". There are many of those,
Okay, so... I found a topic already posted about a weird taskbar issue involving it being wholly unresponsive...
My problem is similar, but not exactly the same, and it doesn't render my taskbar useless, it's just an annoying bug that seems to be completely random. Essentially, some programs seemingly spontaneously develop this problem, and sometimes a quick series of alternate right-/left-clicks can fix it, but not always.
When I want to minimize a program to my taskbar, I almost never use the underscore at the top-right of the window. If the window I want to minimize is in focus, I usually click the focused window's taskbar icon to minimize, which almost always results in a successful minimization. Occasionally, the window doesn't minimize, but it does defocus the window so that nothing in my taskbar is selected.
Like I said, it seems to happen sporadically with no particular input to cause this behavior, and it has happened with nearly every program I run at one point or another.