I spoke too soon!
Even after uninstalling and reinstalling Graphics card the effects were not showing up in chrome browser.
I ran a simple sprite with water effect in Chrome in debugger and it showed the canvas2d function was not running and browser screen showed no effects while layout showed effects applied.
After some searching online I found out canvas2d is still an experimental feature of chrome and I went to chrome://flags/ and found the canvas2d feature and disabled it and relaunched chrome.
The effects started working and then I went back and enabled canvas 2d and effects are working and debugger now shows webgl is working.
So hope that helps someone experiencing the same problems!
ADDED: If you see a funky green line around your layout when you play the game go back to chrome://flags/ and click on reset to default and relaunch your browser. That got rid of green lines and effects are working again.