I am using Windows 10 64-bit.

>> sometimes whatever you pressed in step 3 disappears,
>
> When Shell is restarted by whatever means, any pending input, whether in response to '>>>' or user input(), is cancelled and
> *should* disappear and not be left to look as if it were processed.  It  consistently does for me.
It doesn't for me.

> > doesn't respond to commands
> 
> When a user-coded input() is active, anything typed *should* be treated as text and not interpreted as a command.
Even before enters?

At the comments of http://inventwithpython.com/blog/2011/11/29/the-things-i-hate-about-idle-that-i-wish-someone-would-fix/ I found someone having the same problem as me, MrValdez ()

This is a relevant part of his comment:
> ANNOYANCE: input() doesn't play well when re-running a script when the script is already running.
> 
> Here's a use case. A student types this program in IDLE:
>
> --
>
> x = input("Typ a word:")
> print (x)
>
> --
>
> They run the code. In the shell window, the student would notice the mispelling. Without exiting the shell window,
> they would go edit the code and then press F5.
>
> The shell would still be running the previous code instead of restarting.
>
> In some of my exercises, the students would sometimes think their code are broken when in reality, they already 
> got the solution. They were just running the older instance.
>
> This becomes common enough that I ask my students to exit the shell window before running their scripts.