One problem I see is that in emacsgtkfixed.c we set up the preferred
size of the frame widget and take the width and size from our
min_width/min_height size hints.  From the mutter log we know that these
are broken so maybe GTK does something weird with them.  Please put
breakpoints at the lines

   if (minimum) *minimum = w;

and

   if (minimum) *minimum = h;

within the #else parts of emacs_fixed_get_preferred_width and
emacs_fixed_get_preferred_height in emacsgtkfixed.c and tell me which
values are assigned here: Once for a good scenario and once for a bad
one.  Here I get 0 initially and later on 110 for h and 90 for w.