Hi Jan,
This is not strictly a GTK bug, but could you take a look at bug#2715?
http://emacsbugs.donarmstrong.com/cgi-bin/bugreport.cgi?bug=2715
The basic problem, I think, is that when the font size changes, Emacs
tries to change the pixel width and height of the frame, keeping the row
and column numbers unchanged (xterm.c:8116). However, this fails when
the frame is maximized---in that case, we can only change the row and
column numbers, and the pixel width and height cannot be changed.
However, I am not sure how to fix this. Maybe you can suggest a
solution?