Hi Craig,
Thanks for the file.
The problem is that there are a couple of islands in your user map with < 2 points, and this is causing an exception when we try to export them as polygons in a Shapefile. We really should protect against this, and I will make sure that a fix for this is included in the next maintenance release.
In the mean time, the workaround is to ensure that these islands are removed from your user map before the export is attempted. The easiest way to do this is probably to remove all islands and shorelines from your user map, delete the rogue islands from the map boundaries in the original map project, regenerate the project and add just the shorelines from the project back into your original user map. This means you can keep all the rest of your edits in the map (isobaths and so forth).
Matt