Oh god the exact same thing has just happened to me. I got a replacement hard drive, swapped out my old one, only to find that my time machine backup was incomplete 😟
At first I thought I had accidentally excluded System Files, so I swapped back in my old hard drive and checked. Nothing was excluded (supposedly). Anyways I found a CNET article telling me to turn SkipSystemFiles to false through terminal so I did that, re-did a WHOLE NEW backup on a new hard drive and system files are still absent!!
So finally at the end of the day I come here and see your comment. Same issue. All my system files in "ExcludeByPath" just randomly. For what its worth, I too have Silverlight installed.
Have you reported the potential bug in the API?