Emulator

Game Name?

Any

Game ID? (right click the game in the game list, properties, info tab)

Any

MD5 Hash? (right click the game in the game list, properties, info tab, MD5 Hash: Compute)

N/A

What's the problem? Describe what went wrong.

Window overlaps the title bar

What steps will reproduce the problem?

Run any game in windowed mode. Note: I use the CLI version, not the GUI
The issue alternates between runs. First time it will be offset, second time it will be normal, third time it will be offset etc.....

Which versions of Dolphin did you test on? Does using an older version of Dolphin solve your issue? If yes, which versions of Dolphin used to work?

Latest GIT as of June 4th 2016

What are your PC specifications? (CPU, GPU, Operating System, more)
Core I7
6 Gig Ram
GTX 770
Fedora 23

Is there any other relevant information? (e.g. logs, screenshots,
configuration files)
Attached