Thanks for your dedication to the tool, Celludriel.
I seem to have a workflow that gets consistent success now. I don't know which of these exactly resolves my former issues, but I was able to make a good 6-7 maps in a row this morning. Things I am doing:
1. Create a new level with only one terrain and save.
2. Always choose a normal 'exit' from the editor. I was in the habit of choosing 'force exit' from the extended period of time when the editor would hang and crash from a normal exit but that seems to be mostly resolved at this point.
3. Run the heightmap tool in administrator mode.
4. Fill-in the bitmap file first and editor terrain second.
My guess is that #2 in the list is the real difference maker. You can see some built-in source control stuff going on when saving a level and perhaps there is some kind of internal locking happening that does not get released when you force exit from the editor.
I do still get crashes when attempting to import heightmaps with a level size of 10x10, but since that is too big for my needs anyway, not a problem for me.
Thanks again, this tool is a huge help to me.