After some communication with the support team the following solved the issue for me:
u1sdtool -q rm -rf ~/.local/share/ubuntuone u1sdtool -c
If you are trying to sync folders outside your ~/Ubuntu One folder please open the Ubuntu One Control Panel, click on the "Cloud Folders" tab and make sure that the folders you want to sync are checked there.
After some communication with the support team the following solved the issue for me:
u1sdtool -q share/ubuntuone
rm -rf ~/.local/
u1sdtool -c
If you are trying to sync folders outside your ~/Ubuntu One folder
please open the Ubuntu One Control Panel, click on the "Cloud Folders"
tab and make sure that the folders you want to sync are checked there.