subfolders in archive

Splitting jumping backwards after download into a separate issue

Subfolders in the archive can be avoided by setting the 'Image filename pattern' in the 'Download archive of images' fieldset of the Bulk Operations view settings. Setting it to something like [field_name_of_cck_field-filefield-filename] will just take the all the images being downloaded and chuck them in the root of the zip (obviously look at your token replacement patterns for your own case).

If you are using this module without views operations, to remove the subfolders you can change this line:

$pathname = token_replace_multiple($context['settings']['filename'], array('global' => NULL, 'imagefield_archive' => $file, 'node' => $file->node));

to simply:
$pathname = $file->filename;

Closing this as I don't plan to support this module.