iCloud Synching Scrambles Safari Bookmarks
This sounds like a Safari issue, not an iCloud or Bookmarks issue, to verify that, lets reset Safari back to scratch. This wont delete any bookmarks. You may want to clear the history too.

How to fully reset Safari on your Mac


  Remove Safari’s configuration folder:
  
  
  Open the Go menu in the OS X Finder
  Hold the Option key and choose the Library option that appears
  Move the “Safari” folder in here to your desktop
  
  
  Remove Safari’s window state:
  
  
  Open the Library > Saved Application State folder
  Locate the “com.apple.Safari.savedState” folder
  Move this folder to the trash
  
  
  Remove Safari’s application caches:
  
  
  Open the Library > Caches folder
  Locate all folders that begin with “com.apple.Safari”
  Move these folders to the trash.
  
  
  Remove Safari Cookies configurations:
  
  
  Open the Library > Cookies folder
  Remove the file called “com.apple.Safari.SafeBrowsing.binarycookies”
  
  
  Remove Safari’s preferences:
  
  
  Open the Library > Preferences folder
  Remove any file that begins with “com.apple.Safari”
  
  
  Remove user plug-ins:
  
  
  Go to the Library > Internet Plug-Ins folder
  Move all items from this folder to your Desktop (or elsewhere)
  
  
  Remove global plug-ins:
  
  
  Go to the Macintosh HD > Library > Internet plug-ins folder
  Move all items out of this folder except the following plug-ins:
  
  
  *

Default Browser.plugin
iPhotoPhotocast.plugin
Quartz Composer.webplugin
QuickTime Plugin.plugin

  
  *


That may help with the issue you are having via Safari and not your bookmarks.