Like Zak I use only the Portable version which puts nothing in the registry but you may have another copy of the settings file buried in some Users folder from a past install that was not properly deleted. To find out do a Windows File Explorer search (include hidden files/folders) for "MusicBee3Settings.ini" which holds the entries that would affect this for the Installer or Portable version.
I've looked for that file, sadly i didn't find it.
What's weird is that i setup a virtual windows 10 machine, installed latest MusicBee v3.5 portable, copy over it the latest v3.6. Then started as a new blank library, unchecked "scan on startup" on Settings and added a few mp3 files to the library using "Scan Folders for New Files".
Restarted the virtual machine, opened Task Manager and Resource Monitor/Disk tab and finally started MusicBee, unfortunately the same behaviour occurs. (This is using a USB drive with a few files, before it was internal HDs).
@Steven, i'm aware this is low priority (perhaps i'm the only one that is experiencing this) and that there is no support for v3.6 currently. But i'm at your service to try any test you may feel would be worthwhile.