I was just thinking about this post earlier today. I'm sorry to hear it hasn't resolved. I've seen a few posts here this week from folks having issues with other system settings resetting on their own after a reboot (all file access, wifi control, etc.).
I am wondering if there's any chance you've changed the default app settings (not the in-app settings) for the clock or any other system apps. I'm grasping at straws here, but for example the option, Pause app activity if unused is disabled by default for the clock, and the Battery should be set to Unrestricted. Not that I can see how either of these settings would result in what you're experiencing, but just trying to eliminate possible factors.
For what it's worth, your post had me checking my clock app daily for any changes...and none seen so far.