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I'm having similar problems. Although the syncing seems to work one-way from my iMac to Air (into a folder within bookmarks.) The Air's bookmarks just don't sync at all.

I've fed it back, hopefully they'll iron this out in an upcoming beta.
 
Fix for iCloud bookmarks

I've been having the same issues with bookmarks not syncing to my iPad/iPhone. I found a solution that said to turn off Bookmarks sync under iCloud in System Preferences on your Mac, then turn it back on. This did the trick for me and bookmarks are now syncing to both devices properly. Hope this helps.
 
I've been having the same issues with bookmarks not syncing to my iPad/iPhone. I found a solution that said to turn off Bookmarks sync under iCloud in System Preferences on your Mac, then turn it back on. This did the trick for me and bookmarks are now syncing to both devices properly. Hope this helps.

At the time I wrote that post I wasn't running the dev os x build. Thanks for the reply though. Glad it worked.
 
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