I’m not sure how thumbnails work with s3 offload, but I’m guessing they don’t automatically get pulled on regeneration. However, the more advanced use of smartcrop should work. Try adding an image into post content at full size, then use css to set the width and height. smartcrop should step in and make sure the image crops live in-browser.
I’ll look into S3 offload. it may be possible to trigger a cache refresh.
Having read through the plugin’s source, it looks like it should be working. My guess would be that S3 doesnt immediately invalidate resources on update, and you may have to wait for the cropped resources to expire in the s3 cache for the updated thumbnail to take effect.
If not, this appears to be a bug with S3 Offload, as the wp_update_attachment_metadata filter on line 189 of amazon-s3-and-cloudfront.php should be uploading the new thumbnails to s3. I’d suggest filing a bug report with Delicious Brains.