This problem is no longer reproducible. For the last few weeks, iCloud Safari bookmarks syncing has been working OK for me. However, I don’t test it every day.
SHORT VERSION WITH WORKAROUND
In order to see recent bookmarks changes made on other devices in Safari on your iPhone or iPad running iOS 9, you must relaunch Safari (double-click the home button, then in the application switcher which appears, flick the Safari tile upward, then relaunch Safari).
This seems to affect all Safari users, whether or not you are using BookMacster, Synkmark or Smarky. The same behavior occurs if you change bookmarks directly in Safari, as explained below. We reported this as a Bug 22932240 to Apple on 2015 Oct 01, as follows:
In iOS 9, when using iCloud Safari syncing, Safari bookmarks are not pushed from iCloud automatically, no matter how long you wait. They don't show up until you forcibly relaunch Safari. This was tested most recently in iOS 9.0.1 (Build 13A404).
STEPS TO REPRODUCE
1. On a Mac running, say, El Capitan, switch on iCloud Safari syncing.
2. On an iPad running iOS 9, connected to the same iCloud account, switch on iCloud Safari syncing.
3. Wait 20 minutes or more.
4. Verify that Safari bookmarks have merged OK.
5. On the Mac, make a change to bookmark(s).
Changed bookmark(s) should appear in Safari on the iPad within a few minutes. This worked correctly in previous versions of iOS. Bookmarks changes appeared after 15 minutes at most, surprisingly, even if the bookmarks "menu" was currently being displayed.
You can wait as long as you want. One time, I tried waiting 48 hours. Still the bookmarks change do not appear. However, if you force-quit Safari on the iPad by "flicking it up" from the application switcher, then re-launch Safari, the new bookmarks changes always appear after a few seconds.