I'm basing this post on FMP 5.5 which I think is the same in this detail as FMP 6--which I don't have.
The fields exported is not determined by your layout.
Select Export Records from the File menu and export your data to your text file without using your script. During this process you can change which fields will be exported.
Now open the script in script manager and close the script again. When you close it, filemaker will ask if you want to keep or replace the current export order. Choose replace.