I was running rsync through ssh and it was failing with the lovely message
protocol version mismatch - is your shell clean?
A little digging on the man page I found this gem under the Diagnostics section:
rsync occasionally produces error messages that may seem a little cryptic. The one that seems to cause the most confusion is "protocol version mismatch - is your shell clean?".
This message is usually caused by your startup scripts or remote shell facility producing unwanted garbage on the stream that rsync is using for its transport. The way to diagnose this problem is to run your remote shell like this:
rsh remotehost /bin/true > out.dat
then look at out.dat. If everything is working correctly then out.dat should be a zero length file. If you are getting the above error from rsync then you will probably find that out.dat contains some text or data. Look at the contents and try to work out what is producing it. The most common cause is incorrectly configured shell startup scripts (such as .cshrc or .profile) that contain output statements for non-interactive logins.
Logging into the server immediately revealed the problem. An errant echo statement in .bashrc meant to annoy my coworker when he logged into the system. With my little prank removed, rsync worked flawlessly.