The dotted line cube indicates the total possible travel in X,Y and Z as determined by your limit switches or soft limits as defined in the configuration. Those are G53. G54 is the work offset and must fit within those defined limits. If the cutting path does not reflect the G54 work offset location you have set then you need to hit the Regen button to allow Mach to recalculate the paths. If you set the G54 work offset before loading a program then that is not necessary. However if you loaded the program first then set your G54 work offset then a regeneration of the tool path is necessary.