Some users are experimenting missing files and folders on their desktop clients. These files and folders appear checked on console tree and can be seen via browser. So they exist but for some reason disappear from desktop.
The only way to recover from this is to uncheck all on console tree and check it again.
Client version: 2.3
Client operating system: windows 8
Operating system: ubuntu 14.04
Web server: apache 2.4
Database: MariaDB 10
PHP version: 5.5.9
ownCloud version (see ownCloud admin page): 9.1.4