We have a bug in matplotlib here:

matplotlib/matplotlib#1126

Steps to reproduce:

Run ipython --pylab=qt. Type "plot([1,2,3])". A window is displayed. Press the save button. The save dialog will flash momentarily and then disappear.

I'm not entirely sure what's going on with this one, but it does appear to be some sort of interaction with the inputhook that ipython --pylab=qt installs.

Using git bisect, I was able to track this down to 76f9a74 in ipython. If the problem is better solved from the matplotlib end, we're happy to do it, of course, I just don't know enough about these inputhooks to even begin to arrive at a solution, unfortunately.