What steps will reproduce the problem?

Adding files to a local annex set up to sync to a remote S3 one

What is the expected output? What do you see instead?

It syncs, but maxes out the uplink

What version of git-annex are you using? On what operating system?

3.20121112 on Debian testing

Please provide any additional information below.

The man page lists how to configure rate limiting for rsync, not sure how to do it for this