Issues with regions using the Spaces Dashboard module
In case anyone still cares about this ...

You cannot drop blocks into empty regions, because they are empty. You can tell the dashboard settings to show all regions always, and then use CSS to hide the regions you dont want to be droppable ever via display none in CSS i think. Thats what I did.

The save button issue you would have to debug with Firebug and maybe a php profiler. You need to be sure the zen theme has allllll the html and css needed by the Gingko theme as lined out in that blog post above for the various JS actions to get processed correctly for the dashboard editor.

I followed the same tutorial for a Zen subtheme, spaces, dashboard and spaces_node and got it all working -- migrating to D7 looks like a pain in the future.