This behavior still exists in Ubuntu 14.04 LTS and VMware Player 7.1.2. The file /home/user/.local/share/recently-used.xbelwill be emptied from time to time and every time you log out, thus the library / list of VMs will be lost.
This only happens if you have deactivated 'Record file & application usage' in Ubuntu System Settings 'All Settings / Security & Privacy / Files & Applications'.
If you activate 'Record file & application usage' your list of VMs will not be lost anymore, as the file 'recently-used.xbel' will no longer be emptied. I'm actually very happy to have discovered this, because before I had to manually restore the list of VMs dozens of time.