What version is your PBX? Please let us know so we can figure out what could cause the deletion of your contacts.
Also, for your second question, the parameter "Can manage the company phonebook" should be enabled from Extensions > double click on preferred extension > Rights. This should be done on all the extensions that have the need to customize the company phonebook.
I have changed some internals to allow them to modify company contacts but the remaining had already this settings.
Actually the company conctact list has only 1 contact while the other seems to have returnend to populate the windows client. For some Reason the windows client
1) Has lost contact but has then regained them
2) Conctacts are not bein transfered to the main contact list