I'm on Xubuntu 14.04 and using chrome 39. When cold starting chrome, webgl works fine, but after the screen locks, webgl stops working, and chrome://gpu shows webgl as not available. I have also tried having a webgl app run when the screen locks, but chrome just freezes up and I have to restart it. Firefox is fine and works perfectly with webgl, and I'm on latest Intel drivers.
- Install the latest version of the (tested) proprietary driver for your grahics card via Additional drivers in Xubuntu.
- Go to chrome://flags/ with the latest version of Google Chrome.
- In this page, enable Override software rendering list and relaunch Google Chrome.
- Go to chrome://gpu/ and see if WebGL is active.
- Look if your problem is gone or not.