Having the same problem. I made a new marker for gathering after the update and when I zoned out and came back later they were gone. I can make them again and they will show up but as soon as I zone out and back they are gone again. The zones where I didn't make a new marker are fine. I have noticed that the zone I'm losing the markers in will have the markers for whatever previous zone I was in.
Edit:
Just found this thread http://www.mmominion.com/Thread-Post-Pat...es-Updates. So it's a known issue.
Edit:
Just found this thread http://www.mmominion.com/Thread-Post-Pat...es-Updates. So it's a known issue.