I have seen the same thing: if Manager configuration is left open and saved at a later time, user-defined settings like call waiting, do not disturb, call forwarding, etc., revert to previous settings.
Also, if you are running phone manager or softconsole, beware of the short-cut keys. there are shortcut keys on the keyboard that can turn features on and off and are sometimes pushed inadvertantly, especially if softconsole or phone manager is set to pop on an incoming call.
Great works are performed, not by strength, but by perseverance.
-Samuel Johnson