The Admin Console and its communication with FileMaker Database Engine has improved from version to version. For FileMaker 10 and especially 11 it is slowly becomming really reliable.
In previous versions, 7, 8, 9 and to some extent 10 you could have situations where the frontend lost all contact to the base, and "forgot" to store the changes.
With FileMaker Server/Server Advanced 11 FileMaker has included a service that keep checking that the admin backend is actually working.
So you have already desided to to the right thing to solve your problem: Upgrade to FileMaker Pro 11.
If it is on Mac 10.7 you must make sure not to try to install the original FileMaker 11 Server. You need the very latest version.
Installed FM11. Problem solved this way. For FM9 it will remain a mystery.