The Sinar 54H takes a black reference shot prior to the multishot sequence only when necessary. Necessary means whenever the exposure time is altered in the software. So, as long as the exposure time remains constant in the software, then this extra frame for black reference calibration only occurs once. As soon as you change this exposure time setting, then it will automatically take another black reference calibration shot at the beginning of the next multishot sequence. There is no beep, but the message window on the computer screen does inform you when this occurs.
Of course, you also have the option of eliminating this black reference shot during the multishot sequence, by doing it separately before the actual shot.