It took me a couple of days of debugging to figure this out, so I wanted to bring it up in case anyone else ran into a similar issue. I'm on the latest CRAN release of Shiny (version .6?).
It appears that passing a zero-length logical to updateCheckboxInput causes the Shiny interface to more or less freeze up (or at least act in a very strange manner, updating some parts of the page but not others). Obviously there are very few situations where you'd want to pass a zero-length logical to a checkbox, but accidents happen, and it would be helpful if an error were thrown indicating the problem.
This line causes the problem to occur whenever I insert it. Adding It seems to affect random (or possibly all) objects on the page, not just those connected to the checkbox via reactive relationships.
updateCheckboxInput(session, "checkboxControlName", value=logical(0))
Otherwise, Shiny's been everything I could have asked for! Thanks for a great product.