The default backend (Qt4Agg) seems to be changing my figure size. The problem does not occur in AGG, TKAGG, or WEBAGG backends. I have not tested others.

Matplotlib version: 1.5.3 installed via anaconda
Python version: 3.5.2
Platform: Windows 8.1

The following is the minimal code I came up with that will reproduce the problem:

import matplotlib.pyplot as plt
fig = plt.figure()
print('size before:', fig.get_size_inches())
fig.canvas.flush_events()
fig.canvas.flush_events()
print('size after:', fig.get_size_inches())

This produces console output:
size before: [ 8. 6.]
size after: [ 8. 5.95]

In more general use this typically arises after a couple of frames have been displayed, and specifically causes a problem when making a movie from those displayed images: the output rolls by 5 pixels from frame to frame. Playing back the resulting mp4 looks like an old analog TV with the vertical sync out of whack.

BTW, one workaround is to call fig.set_size_inches(8,6) after the second flush above but before any frames are generated or grabbed, as the size does not seem to get changed again.