We currently don't support sync of files outside the home folder.
You can take a look at this bug, mark it as affecting you and add comments:
https://bugs.launchpad.net/ubuntuone-client/+bug/854143
Thanks for your report.
** Changed in: ubuntuone-client (Ubuntu)
Status: New => Invalid
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https://bugs.launchpad.net/bugs/1063232
Title:
nautilus integration does not work properly with symlinked folders
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