Hello, miguel.

Thank you for contacting us.  Indeed, Smarky, Synkmark, Markster and BookMacster go to great lengths to push changes into iCloud.  But Apple has changed the protocol for some users recently, and if you happen to be one of these users, and have not been using version 2.4.12 or later of our app for the last couple weeks, you will get the misbehavior exactly as you have described.

If you have used an earlier version of Synkmark recently, you should first clear out all bookmarks and start over again, as you have described, this time using version 2.4.12 or later.

If you've been using 2.4.12 or later, we need to investigate further.  Please tell us what version of macOS you have, an whether or not you are on the new protocol.  To learn the latter,

• Run the Terminal application (which is in /Applications/Utilities).  A window will open.
• Copy and paste the following command into the Terminal window:

/usr/libexec/PlistBuddy -c "Print Sync:CloudKitMigrationState" ~/Library/Safari/Bookmarks.plist

• Hit return.  I expect that a number: 0, 1, 2 or 3, or a Does Not Exist message will appear on the next line.  What do you get?

If you prefer, you may send the answers to and we shall handle it privately.

For your information, 0 or Does Not Exist indicates that you are still on iCloud's old protocol.  3 indicates that you are on the new protocol.  1 or 2 are rare; I've never seen a 1 and only seen a 2 momentarily when initially connecting from a new macOS 10.12 user account to a iCloud account which was on the new protocol.

Also, a testing tip, in case you have not already discovered this:  We've seen the delay before Safari bookmark changes appear on other devices vary randomly from 0 to 20 minutes.  You can usually, but not always, coax the changes to appear faster by relaunching Safari on the receiving device.  (To relaunch on a iOS device, activate the app switcher and flick Safari upward to force quit, then tap the Safari icon on your Home screen.)