When PGF is active, the tool only yields Mists, NW and Siege Keys for me. When disabled I see other dungeons as well. I even tried without any filter except partyfit and this is still the case. Is there something broken with the new dungeons?

I opened Stanzilla/WoWUIBugs/issues/661 for further investigation.

There seems to be a Blizzard bug that whenever you enter a search expression like "5-7", only dungeons from previous expansions are shown and TWW ones are missing.

PGF is not removing any new dungeons. You should see them same behavior with PGF on and off.

Seems to be fixed with todays maintenance.