File Structure always Flattened!

[Jay Smithson]

Hi
I'm quite new to this but am converting a set of html files and images to epub.
In the source, all my images (a lot of them!) are in a folder called 'images'.
When converted to epub, the zip contains my text/html files and all of the images at the top level - the images folder has gone.
I have noticed the option box 'flatten file structure' but this is NOT checked.
How can I get Calibre to leave my images in their 'images' folder?
What else could I be doing to make it behave this way?
Thanks, Jay