It took me a little while to wrap my head around this too, but the RJS is translated to Javascript automatically for you, returned to the browser, and then executed in the browser - and all this happens asynchronously with regards to user actions in the browser.
Now, what makes everything fire off to begin with, is just as you said - a button, link, or internal timer (like with periodically_call_remote).
Getting back to your original problem - what happens if you comment out the shake effect, and only do the div replacement with your partial. Does the cart update correctly?
Jeff softiesonrails.com