This issue only occurs when running the mod in actual Minecraft. When debugging in Eclipse it works as expected.

Confirmed!
Steps to reproduce:

1. Create new flat world
2. Place 2 markers close to each other (possibly within the same chunk?)
3. Exit the world and log back in
4. One of the markers would be gone.
5. Unconfirmed step: delete the remaining marker, log out and log in, and the other one would show up.

Can't reproduce anymore :(