Thanks Paul.
It helped a lot. I have exactly the same behavior.
After Nvidia binary become XRandR compatible, I encountered the same problem (feature!!??). Before that RandR reports one monitor with  3360x1050 monitor. (i have 2 22" 1680x1050 monitor in TwinView)
Also, If application window size is about 75%-80% of monitor resolution size it start maximized.  I start to wright simple Gnome app to find out exact window size.


On 23 August 2012 21:15, Paul W. Frields <stickster@gmail.com> wrote:
On Thu, Aug 23, 2012 at 01:04:09AM +0200, Kernel Guardian wrote:
> First of all:
> I have no intention to initiate a new discussion on the usefulness of the
> GNOME 3 desktop environment. I just want to find a solution for my problem.
> In fact, I have a huge problem with OpenGL applications. The main window is
> always maximized at startup, although OpenGL context using the given size
> in the configuration file. The rest of the main window is black.

Not sure if this thread might help:
http://lists.fedoraproject.org/pipermail/desktop/2012-August/007602.html


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