Here is 100% reproducible test case: run

emacs -q -mm -l test.el

with the attached test.el, and notice that the mouse pointer
is banished to the middle of the frame.

Afterwards manually executing `M-x toggle-frame-maximized RET' twice
fixes the frame dimensions.

This happens in GNU Emacs 25.0.50.1 (x86_64-linux-gnu, GTK+ Version 2.24.23)
Repository revision: 52afe0cfa248053c96e26bc67bdc427945358655
Windowing system distributor `The X.Org Foundation', version 11.0.11501000
System Description:	Linux Mint 17 Qiana

================================================================
`window--dump-frame' outputs:

frame pixel: 1366 x 718   cols/lines: 170 x 42   units: 6 x 10
frame text pixel: 1350 x 718   cols/lines: 168 x 42
tool: 0  scroll: 0/0  fringe: 16  border: 0  right: 0  bottom: 0

#<window 3 on *scratch*>   parent: nil
pixel left: 0   top: 0   size: 1366 x 708   new: 708
char left: 0   top: 0   size: 170 x 71   new: 71
normal: 1.0 x 1.0   new: 1.0
body pixel: 1350 x 698   char: 225 x 69
width left fringe: 8  left margin: 0  right margin: 0
width right fringe: 8  scroll-bar: 0  divider: 0
height header-line: 0  mode-line: 10  divider: 0

#<window 4 on  *Minibuf-0*>   parent: nil
pixel left: 0   top: 708   size: 1366 x 10   new: 0
char left: 0   top: 71   size: 1366 x 1   new: 1
normal: 1.0 x 1.0   new: 0
body pixel: 1350 x 10   char: 225 x 1
width left fringe: 8  left margin: 0  right margin: 0
width right fringe: 8  scroll-bar: 0  divider: 0
height header-line: 0  mode-line: 0  divider: 0

================================================================
`window--dump-frame' outputs after manually calling
`toggle-frame-maximized' twice that fixes the frame dimensions:

frame pixel: 1366 x 718   cols/lines: 227 x 71   units: 6 x 10
frame text pixel: 1350 x 718   cols/lines: 225 x 71
tool: 0  scroll: 0/0  fringe: 16  border: 0  right: 0  bottom: 0

#<window 3 on *scratch*>   parent: nil
pixel left: 0   top: 0   size: 1366 x 708   new: 708
char left: 0   top: 0   size: 227 x 71   new: 71
normal: 1.0 x 1.0   new: 1.0
body pixel: 1350 x 698   char: 225 x 69
width left fringe: 8  left margin: 0  right margin: 0
width right fringe: 8  scroll-bar: 0  divider: 0
height header-line: 0  mode-line: 10  divider: 0

#<window 4 on  *Minibuf-0*>   parent: nil
pixel left: 0   top: 708   size: 1366 x 10   new: 0
char left: 0   top: 71   size: 1366 x 1   new: 1
normal: 1.0 x 1.0   new: 0
body pixel: 1350 x 10   char: 225 x 1
width left fringe: 8  left margin: 0  right margin: 0
width right fringe: 8  scroll-bar: 0  divider: 0
height header-line: 0  mode-line: 0  divider: 0

================================================================