iCloud Safari bookmark syncing errors (iPad Mini/iPhone 3GS and iMac)

The only way I can get my bookmarks to sync is manually through iTunes.

With iCloud, the bookmarks all get duplicated and distorted. On my iMac (OSX 10.8.2 Safari 6.0.2 [both latest]) all my bookmarks are on the bookmarks toolbar in folders (with some folders in the folders). When I sync via iCloud, most of the bookmarks in the folders, and the folders in the folders, just get copied into the root directory on the iPhone (5.x) and iPad (6.0.1) bookmarks, making them impossible to use as it's several hundred links in a long list rather than in folders. Through the iTunes sync they copy over perfectly!

How can I fix this? Turning off Safari sync sadly also removes Reading List and just generally makes it more awkward. And I'm not going back to Xmarks or anything similar...