I am using Windows running Python 2.7.5 (and IPython 1.1.0) with Matplotlib 1.3.1, using the Qt4Agg backend. When I run

import matplotlib.pyplot as plt
plt.ion()
plt.plot([1, 2, 3])

a (blank) figure window is immediately opened and is unresponsive ("loading" cursor on mouseover, can't move window, etc.). This happens in both Python and IPython, and whether I import MPL directly or via pylab.

If I call plt.pause(2), the plot itself is drawn and the figure window can be moved, but it may be moved only until the pause command expires. It seems that dragging the window causes the pause to last longer, i.e. the GUI main loop seems to be blocking the 'countdown' from happening.

If I omit the plt.ion() and call plt.show(), a figure with a plot is shown as expected.

Strangely, when using a Python 2.7.5 interpreter embedded in Spyder (a scientific python IDE), interactive mode works as expected. If I run the startup script provided by Spyder (scientific_startup.py) in Python or IPython, it does not fix the issue, so I'm unsure where this difference in behavior is coming from. All three interpreters use the 'Qt4Agg' backend.