I opened a new file with 15 replicates showing in the Peak Areas > Replicate Comparison plot. When I right-clicked to order by the acquired time, there was no "Order By" menu item. This was pretty shocking to me, since I demo this so much. Eventually I realized that nothing was checked in the "Group By" menu. When I checked "Replicate" in that list, then the Order By menu came back.

This was so confusing because the plotted data was clearly not grouped but showing the full replicate comparison. It took a while to realize that this could be the case even when the menuing was confused about the Group By state.