I just thought I'd follow up on this topic further. I've got a solution to this problem. It's not pretty but it does the trick.
My IP is dynamic (as I'm sure most average folk's are), and whenever my internet or router is reset for whatever reason, I get assigned a new IP address. Every time the IP changes, Mapwriter looks at it as though you're playing on a fresh world save resulting in everything disappearing.
The work around is to log onto your world after your IP resets and back out. This creates a new folder for the new IP address. Then go into your Saves folder followed by the mapwriter_mp_worlds folder. Copy everything from the old IP folder into your new IP folder that got generated and overwrite everything when prompted. All markers and explored areas are back in your map again.
I don't know if this would really be considered a "bug" as it could be a structural property of the mod itself. I just thought I'd let others know the about the solution that might be having a similar issue.