In order to better determine what the issue might be we need to get some debug logs. You can do that by running this command in a Terminal:
Go through the steps to reproduce your issue. The log you can find at ~/.cache/ubuntuone/log/syncdaemon.log
echo -e "[logging]\nlevel = DEBUG" > ~/.config/ubuntuone/logging.conf; u1sdtool -q; u1sdtool -c
My first guess would be bug 545350
Note that attaching syncdaemon.log will show filenames you are attempting to sync with Ubuntu One. If you do not want this to be public, please obfuscate those names. Or you can file a bug and mark the bug as private and this bug report will only be available to you and the Ubuntu One team.