By default, when FlowJo layout editor is used to make a histogram overlay, the Y axis scaling is defined as "unit distribution". This is one of 3 options available for overlay scales. You can get to these settings by double-clicking any histogram overlay in FlowJo for Windows:
This is a scaling option which normalizes for the area under each curve and scales the Y axis accordingly. In this mode, the Y axis represents the % of cells found at a given bin.
For example, at the 10^0 fluorescence level, the green curve has approximately 1% of the events.
This scales each curve to mode=100%. In this mode, at 10^0 bin for the green curve there are roughly half as many cells as in the mode.
This will let you scale the histograms on a traditional, #count Y axis. You can choose the top/bottom values for your axis. The Y axis indicates how many events are at each bin.