Note that gates will not show up if you choose a different compensation or change your scale settings.

"Show gates" will only show gates that were drawn with the same X and Y axes that are showing. In other words, if you drew a "live cells" gate with the X axis as FSC and the Y axis as SSC, but your working illustration is showing the X axis as "P-Stat1" and the Y axis is "SSC", then you won't be able to see the gate for the population "live cells" because the axes aren't the same.  Your gate will still be shown if your X axis is SSC and Y axis is FSC.

So make sure that your X and Y axes match the gate that you want to see by going into the gating applet (click "Edit" on Populations), selecting the gate you want to see by clicking on it to highlight it in the list of gates, and checking the X and Y axis labels. When you go back to your working illustration (Save & Return), set your X and Y axes to match what you saw in the gating applet and click "Update Plots". You should see any gates that were drawn for those axes on your working illustration plots.

Note that gates will also not be displayed if you are choose a different compensation or if your scale settings are different from the ones used when drawing the gate.