Hello Adrian!
Thank you for your messages.
Actually we have fixed the issue with attributes generation and now Store Manager populates 'attribute_shop' table as well.
Please make sure that you have associated your attributes with the exact stores:
http://screencast.com/t/Z5J4QbZZou8
By the way, we have extended your trial license for 2 weeks so your could continue using the Store Manager ;)
You can find your license key and download the application from your license account at:
http://license.emagicone.com