John
AFAIK to use FM3 you need to
1. Run a the app without FM3 to ensure that all files are in sync with the dictionary
2. add fm3
3. compile and run the app which creates a upg file with the current (clean) status of all the files
4. After any changes FM3 will update from the base correct state and update the upg file
What I think you have done is have tables which are not in sync with the current dictionary and no base upg file.
This certainly is the way I have always worked (doesn't mean I'm right, but I've never had a problem).