So you mean, bookmarks are synchronized, but Fast Dial doesn't use the newly created (synchronized) bookmarks?
Fast Dial uses special bookmark annotation "fastdial/home" on the Fast Dial bookmark folder. Probably Xmarks doesn't synchronize this annotation. I haven't used Xmarks, but I had heard that Firefox Synchronize correctly treats Fast Dial bookmarks. You can go to Fast Dial preferences and "Select" a bookmark folder to be Fast Dial home.