When you use the disconnect from server button, server is notified you are no longer online (and if some orders didn't get to the server yet, they will be sent before disconnectin, AFAIK).
When you just close your client or lose connectivity (like when putting the laptop to sleep) server doesn't know and some of your orders might not be acknowledged, and other players see you as online (if someone tries to whisper to you I think server finds out your offline, and the whisper gets to the general channel).
There is also the issues you were describing about having to completely restart FO. All that is avoided if you just disconnect from server if you're not playing.