System Storage Taking Up Way Too Much Space in macOS Sierra

I've encountered a problem on my brand new MacBook, but haven't been able to find a solution after working on it for most of today. In a nutshell: When I go to "About This Mac > Storage" the System files were taking up a whopping 90+ GB of my hard drive. Here is a screen shot:

I also noticed that, unlike on my wife's MacBook Pro, I had no individual listing for iTunes. I could reach the iTunes folder through Documents on the left side, but the contents of the folder were grayed out. As an experiment, I copied then deleted my entire iTunes Library from within iTunes. After I did that, my Storage report looked like this:

Now the System files are down around 8 GB. (The Documents content jumped up dramatically because I copied my iTunes Library to the Desktop.) Unfortunately, I haven't found a way to establish the separate entry for iTunes in this window. When I move things back into iTunes, they count again toward the System storage amount. And I still don't have a separate iTunes entry.

I would like to be a huge fan of Optimized Storage, but this set-up of counting iTunes media as "system files" seems problematic. And I have no idea why it reports storage content accurately on my wife's Mac but not mine. Unfortunately Apple Support was not very helpful when I contacted them this afternoon. The agent suggested reinstalling macOS Sierra, which I did, but it didn't solve the problem. Some help would be appreciated, Apple!