version: 2.0.0b1+1773.g3590ce2, installed from source
OS: OSX 10.11.6
inside an ipython shell...

clf()
gcf().set_size_inches([4,4], forward=True)
ax = subplot(111)
plot([],[])
title('title')
xlabel('x label')
grid()
subplots_adjust(bottom=0.12, top=0.9)
draw()
show()

what happens to me: with gtk3, running this script the first time, the window pops up, everything is fine. If I then run this script again without doing anything else: the window doesn't change size, but the figure canvas does, pushing the title and the top part of the plot above the top of the window. If I then grab the window resizer and change the size of the window, I see the entire plot (so that signal works).

with gtk2, the same behavior occurs except: the part of the canvas that disappears is the bottom of the plot instead of the top.

As an aside, when this happens, before resizing the window, the zoom-to-rectangle function grabs a rectangle that is offset from the mouse pointer.

Hypothesis: the code is counting the toolbar extents as part of the size of the canvas.

[edited to add code markup tacaswell]