Hi, Chris:
I want to restate what you are describing, so I can be sure I understand the problem.
You have form library with some XML files in it that were created via Qdabra's XLS to XML tool. Your promoted properties for those XML files are populated.
When you create a new form from your template, however, and save the XML, the promoted properties are empty. You are only seeing this on promoted properties that related to fields in your form that use a drop down control type.
Is this correct? If so, this is not a problem I have seen before.
If you go look in the settings for your library, do you see any duplicated column names?
What happens if you re-publish your form to a different, test library?