DayCuts,
It would appear that if the folder doesn't exist remotely based on the listing then the folder was set as "", when syncing "" is equal to CDUP which is why this occurred.
I've decided to change this and attempt to change folders regardless of if the folder exists in the listing as it may have been created and the cache is out dated. Also if the folder simply doesn't exist it won't do a CDUP. though it will still break sync browsing.
Also this behavior existed since sync. browsing was first added.
I did some tests where one site root was / and the other was /temp/ as root and as far as I could tell everything seems to be working fine. Although I did these tests after making the above change so that may be a factor, I'm not 100% sure.
I'll be posting a new build to beta testers today with the above mentioned change, Please give it a try and let me know if you notice any other oddities.
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