Update (Only for making maps for A20 or A21.... 1.0 maps don't have these issues)
The latest update (v0.50.7) corrects the known issues with backwards compatibility that I mentioned above. If you run into any other issues, let us know.
However, please note that part of the correction is added in the default presets, so if you are using an older preset, you may need to either copy the POI Property List and Town Property List from an updated default preset or else start a new preset based off the new default presets. There may be an additional fix added that will make that not necessary, but for now, it would be needed.
EDIT: Okay, so another quick update makes it so your old presets won't be affected. You'll be able to use any older presets without an issue for backwards compatibility.