Can you show a screenshot? Based on your description, it sounds like the standard User Account Control popup that appears whenever a program that accesses the file system is run.
Yes, It look like that, only it says “system ninja” in the top bar of the window. Not sure what you mean by ” User Account Control popup that appears whenever a program that accesses the file system is run.” The window pops up when he launches system ninja, and he has to answer yes to open the program.
Yes, that’s normal behavior when run on newer versions of Windows.
You can set System Ninja to always have administrator rights, so you will only have to click “yes” once. This can be achieved by right clicking on the shortcut, selecting ‘Properties’ and ticking “Run As Administrator” in the compatibility tab.