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Here is my logfile. Just tried it now, and got same error. Only for IE8. FF works great.

Sat Jul 04 19:22:33 2009: Starting Do_update for: ROOT
Sat Jul 04 19:22:33 2009: Executing command: update
Sat Jul 04 19:22:33 2009: Starting Do_update for: +6iaz3
Sat Jul 04 19:22:33 2009: Executing command: update
Sat Jul 04 19:22:33 2009: Starting Do_update for: uWhaz3
Sat Jul 04 19:22:33 2009: Sending local changes to server
Sat Jul 04 19:22:33 2009: New SyncRequest Initialized [POST]: http://sync.xmarks.com/sync/bookmarks... (cleaned body: {"baserev":"31","commands":[{"action":"insert","args":{"bnid":"","name":"Folders","ntype":"folder","pnid":"ROOT"},"nid":"89zaL"},{"action":"insert","args":{"bnid":"","name":"Links","ntype":"folder","pnid":"89zaL"},"nid":"2azaL"}],"log":{"mid":"km7quy"},"manual":true,"view":3}
)
Sat Jul 04 19:22:34 2009: Cleaned SyncRequest response from server: {
"message" : "Profiles Conflict: attempt to create duplicate node 89zaL",
"nid" : "89zaL",
"status" : 445
}

Sat Jul 04 19:22:34 2009: Unexpected error during synchronization: XmarksException [source: internal, id: -50]: putchanges failed during sync attempt
Sat Jul 04 19:22:34 2009: Attaching observers
Sat Jul 04 19:22:41 2009: Recieved WM_COMMAND message: 1068

When I first downloaded xmarks it worked the first couple of times. I have it on two computers with each one using xmarks on FF3.5 and IE8. On my XP desktop both work great, but on my Vista laptop only FF3.5 works now, and I get the error on IE8. I manually downloaded the favorites again as you said to, but then when I tried to sync again, the error showed again. I even uninstalled, rebooted, and reinstalled, and I keep getting the error. Like I said it only happens in IE8 on Vista. The only way I can sync now is to manually download each time. Help!