What part of that quest line are you on? The Time Rifts filter only shows rifts for the current quest stage you're on and dynamically removes them as you complete rifts. An older version of Map Pins showed all the rift locations all the time regardless if you were doing that quest, but that hasn't been the case for awhile now.

If you're just starting that quest chain, you actually need to "use" the map when the prompt comes up after you retrieve the skull. That's when the Summerset rifts will show on your main map.