I've been having this error/bug for the past month now. It usually happens to the new players, if they get a disconnect error, lag out, or I type /kickall "Restarting server" and restart it, they lose their items. This only happens once though. I have no errors in the console, and my plugins are updated.
OmNommNomm Does the map also rollback a little bit, too? Seems like your server isn't saving the map correctly and you are abruptly stopping the process. Try issuing a "save-all" from console prior to restarting/stopping your server.
Multicraft auto-saves for me; this error happens only to a player ONCE. Usually their first time disconnecting, leaving, or server crashing somehow.
I see this is old. But it is happening on my server as well. Even a mod on my server logged out then back in a few days later and soon as he logged in all his items were gone. It is happening to some people every day.