I spent 2 hours this morning marking and labeling ports in the guild hall (palatial) and then went to save it. Just to be sure I went into the folder in maps and it wasn't saved. I tried numerous times with different layers and could never get it to save. It said it saved, but it never actually did. Absolutely repeatable. I made sure i was looking at the correct directory and the right maps folder and it just wasn't saving it at all.
Edits to the default maps do not save properly usually as they are over written each time you zone. Oddly enough I just did the same labeling for guild click ports. If you have downloaded Goods or Brewells then you can edit those and it will save. Also, if you installed to the default location, somewhere under 'users' I believe, that has been know to cause problems because Windows does not like other programs messing with files. It is better to install to a separate folder
If you are going to edit maps it is best to place them in a custom folder you create. Otherwise there is a good chance your edits will be gone whenever the game patches. If you do edit Goods or Brewalls, then you will lose your edits the next time you update them. Just place a copy of the one (or more) map(s) you wish to edit in a folder you create under Maps. Then edit them. If your edits don't stay, then try this: https://everquest.fanra.info/wiki/Tips_and_Guides#Settings_not_being_saved