Ah I didn't consider general attachments for the post. Maybe your plugin is not populating data for the attachment that the SEO plugin needs. It's the attachment method that would be picked up by search engines.
Unless the theme is using images from custom fields.
Good luck with this. Integration is a constant job for plugin authors and it sounds like one of the others from the two plugins need to give this a high priority attention in my opinion. It is a key element in SEO!
Ryan