Thank you for your post.
Without seeing your database file, it sounds like you may have a startup script that opens a template file.
Pull down the FileMaker Pro menu and select "Preferences -> Document...". See if there is a check mark next to "Perform Script" when opening the file. This may give a clue to what is being done. If this is unchecked, then you may have some fields that reference this file. Go through your field definitions, and look for Lookups into this template file.
Also double check your file references ( define relationships) in all of your files.