Resolution x Building Problems

I used to use the version 4.6.1.

The project is basic some scenes, and the main scene we usually use the command Screen.setResolution(1024,768,true) to "fit" to all resolutions and be full screen.

In the version 4.6.1, it worked fine, but for the new project we used the 4.6.4, and when we build the .exe, it don't really fit to the screen (1600x900) it take place in the middle of the screen with a black bar in each side.

We tried open a old project because we thought it could be some setting we were using wrongly, but with the same settings from the old (which is working) still has the problem!!!

Is there anything we could do?

Edit:
We think it mighht be some windows uptade, because it is not changing windows native resolution...

Not in 4.6.1 anymore, only in the beta version works: 4.0.17b, something like that.