While the map itself is lost on every reload, the custom markers I placed on it persist even when starting a new game. Kind of handy, but probably not intentional
Edit: This only seems to happen when old savegames are present. I noticed that conversation options were messed up too (Arhu was willing to discuss the murder at the town gate instead of his study), so I deleted all old saves and started another new game. The markers are gone now.
