Was a
device attached (USB or Calibre Companion)? That connection needs to end gracefully (device says I am done).
Calibre writes its last used settings as it shuts down.
You might check W10
Event Viewer
It might be signaling a Hard Drive or other problem (which would delay the write)
It also may be something else
My last W10 x64 shut down took a bit (longer than usual) of time, but it did end on its own.