I'm not sure if this is related to issue #163.
I was using 1.1.8. When uploading doing a collectstatic to s3, it would run fine the first time. Any further modifications to local files would not be picked up. It would just say "not modified".
It didn't throw any errors, so couldn't debug it. Have no idea why this would be occurring.
I reverted to an older version that I used for one of my older projects (1.1.3) and it correctly picked up modified files.