With tha latest build, this is what I did:
1) Stood in front of a PoK portal.
2) Right click map, Edit, Add Location
3) Typedin "PoP Portal"
4) File, Save Map
5) Move around a bit to make the text pop up (Note sometimes it never does!)
6) File, Save Map again
I then zone, and come back, and my location is gone.