NVidia has released an update for Linux Driver (295.49). This brings new support for GeForce GTX 690 and also fixed performance regression found on previous release (295.40) which i posted on this SlackBlogs as well : Do Not Use NVidia Driver 295.40. This driver also fixed a problem where starting, stopping, and moving OpenGL application windows was very slow on Quadro FX 4600, Quadro FX 5600, GeForce 8800 GTX, GeForce 8800 GTS, and GeForce 8800 Ultra.
I have confirmed that this driver works as intended. I can freely use my desktop as it used to be, so it's recommended to upgrade to this version if you are using a modern NVidia GPU.