The Sequencer software defaults to potential measurements with respect to the reference electrode (wrt RE), however on installation the user is given the option to display potentials with respect to the working electrode (wrt WE). Sometimes this is wrongly selected.
To correct this mistake launch the Mains Configuration program, which can be found under the Start Menu > All Programs > ACM Instruments Version 5 > Configurations. The option to select the way potentials are measured should be titled "Potential Representation: Electrochemical (Potentials with respect to WE)" which needs to be unchecked. If this option is hidden please select the advanced option to display it.