I've seen this - it appears to a be a Finder bug. Are you looking at the contents of your file package by selecting the package in Finder and then right clicking to invoke the menu item Show Package Contents?
If so, that's a problem because Finder caches package contents and won't show you the updates.
Try looking at your file package contents in the terminal using the ls
command as in:
ls -al /Path/to/Your/FilePackage
That should show the new package contents.