Some users are experiencing trouble with the order of the bookmarks under Firefox 18, after running the synchronization job from Firefox for Android.
It appears that users with a larger number of bookmarks (thousands) are more prone to be affected by the issue. However, those with fewer bookmarks (100 and less) to sync are not exempt from having trouble.
Speculation on the issue points toward a bookmark record that behaves abnormally and hangs on the server. Next, the mobile device processes the record and sends the change to the desktop, thus discombobulating the bookmarks.
Although the bug has been first reported in Bugzilla at the end of June, 2012, the issue seems to be without solution for the moment. Also, it appears that there is a spike as far as reports about disorganized bookmarks are concerned.