There is definitely something different going on with your system. I checked and rechecked the behavior of the Safari bookmarks.plist file and it will recreate itself only after a reboot and when accessing Safari for the first time subsequent to the reboot.
I'd be curious to find out what others are experiencing with regard to Safari and the bookmarks.plist file?
My bookmarks sorted alphabetically again today. This post is to keep a record to see if it's consistent in any way. Was not doing anything, Safari was open, one minute bookmarks like I want them, 2 minutes later when I went to them for another choice, alphabetical. So it is NOT associated with booting. And the website I was on at the time was the Wall Street Journal page, so I doubt that they care about my bookmarks.