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It doesn't affect my minecraft window at all. I tested this by doing other resolutions, full screen back to windowed and even window resizer (which works).
It's a known problem with the actual launcher. Hopefully it'll be fixed in one of the next updates.
Until then, you have to resize the window yourself or use a tool that can accomplish this.
The window size thing is a problem for me, too, and I read maybe 2-3 posts about this before. The "known" wasn't meant in an insulting way. Just to clearify that and just in case you might have got it in another way.
Maybe Google needs to start playing FTB.
Edit:
My temporary - quick and dirty - fix for that is a little AutoIt Script. I run it each time after Minecraft ist fully launched. It resizes the Minecraft window (= $title) to the new $width and $height and moves it to the center of the screen.