Similar issues with bookmark synchronization have been raised over and over by many people, on various versions of FF ranging from 3.6 to 9.x, on various platforms (including mobile), all with inconclusive results: see bugs 721635, 718154, 627830, 622588, etc.
I wish I could contribute some definitive bug report, but it's really difficult to reproduce the strange behavior and I often don't find out until several days or even weeks later, by which time the logs are gone.
Unfortunately, the addons.mozilla.org thread where a lot of people reported the same behavior seems to have been deleted when the Sync add-on for FF3.6 was removed.
Similar issues with bookmark synchronization have been raised over and over by many people, on various versions of FF ranging from 3.6 to 9.x, on various platforms
Of the bugs you mentioned, only one of them [1] involves a desktop version of Firefox later than 3.6.3. The reporter there is also syncing with his Android phone and an iOS device. The developers who responded suggest that it might have to do with the Android Sync implementation.
...when the Sync add-on for FF3.6 was removed.
The aforementioned bug notes [2]:
Most of the issues with bookmark sync occur as a result of using the old Firefox Sync add-on and not the version of Sync bundled with Firefox itself.
This would seem to be confirmation that the old Sync addon had issues, but that they should now be fixed. The fact that the majority of reported bugs involving Sync involve Firefox 3.6.3 (or are resolved, like some of the bugs you mention), and that there are none that I can fix involve versions 10 or 11, do not support your assertion that Sync has issues with bookmark sync that "still haven't been fixed."
I understand you want to create a "definitive" report, but it would be good to still go ahead and create a bug about your issue (where actual Sync developers could help you debug it), instead of complaining about it on Hacker News.
I wish I could contribute some definitive bug report, but it's really difficult to reproduce the strange behavior and I often don't find out until several days or even weeks later, by which time the logs are gone.
Unfortunately, the addons.mozilla.org thread where a lot of people reported the same behavior seems to have been deleted when the Sync add-on for FF3.6 was removed.