Hi
I think the easiest way to explain this is that when you publish your form to a library it retains a local copy thet it registers internally as template.xsn. If you need to change this file you need to go into 'modify settings and columns' and click 'Edit Template'.
Make your changes and then that works fine.
The behaviour is, I believe, due to the SharePoint registration process that all form libraries adhere to.
I hope this has been of help
Cheers