NVault has that problem if you keep the vault open the whole map.
This is because NVault doesn't save any data to the file until it is closed.
While it is open, all of the data is stored in memory to be more efficient when grabbing/setting.
When the vault isn't closed due to for example a server crash, all the unsaved data is lost.
With SQLVault, it is stored in the database directly and not in memory, so you will not have this problem.