Different update versions of IPython run in the Canopy GUI application, vs in Canopy User Python at the command line. In particular, notebooks created with IPython 3.x and above will not run in the Canopy GUI, but can be run from the command line.
ipython notebook or
ipython qtconsole, etc, at a Windows/Mac/Linux command line (terminal), with Canopy User Python as your default Python, will run the version of IPython installed in the Package Manager (or equivalently, installed with the enpkg utility).
However, frequently the version of IPython in the Canopy GUI lags behind the version available at the command line. For example, in Canopy 1.5.4, the GUI application uses IPython 2.4, even though IPython 4.0 (Jupyter) is available in the Package Manager and can be used at the command line. A particular version of the Canopy GUI application always uses a particular version of IPython. This is because of the synchronization required between the Canopy GUI and the IPython API. As the IPython API stabilizes, this restriction may be relaxed in future versions of Canopy.
Note 1: an easy way to open a Command Line / Terminal session running Canopy User Python is to use the Canopy GUI's Tools menu.
Note 2: Please do not confuse IPython software version number with Notebook format version number.
IPython version 2.x writes notebook format version 3.
IPython version 3.x and 4.x write notebook format version 4.
Note 3: See also Issues with IPython notebook running in the Canopy GUI application.