the logic was backwards.
@ -456,7 +456,7 @@ var IPython = (function (IPython) {
var callbacks = this._msg_callbacks[msg_id];
if (callbacks !== undefined) {
callbacks.iopub_done = true;
if (!callbacks.shell_done) {
if (callbacks.shell_done) {
this.clear_callbacks_for_msg(msg_id);
}