We have seen this issue a few times, it doesn't seem to always happen, but when it does it does it only for specific shared folders / users.
We're running 5.0.12 on PHP 5.3.10, using MariaDB (MySQL compatible).
We have our users authorized by LDAP and we share folders to them via LDAP groups.
For example, everyone is in the 'Global Cloud Users' group, and we share the various company wide shared folders to that group, with read only access. When it was later shared to 'Global System Administrators' with write access, some of the folders appeared with (2) appended to the name, and I and other admins could write to these, but not the original folders. Expected behavior would be that we have write access to the originally named folder, which happened for some folders. None of the folders or groups have numbers in them anywhere. Weirder, the list of (2) duplicates that I had were different from another admin.