Steps to reproduce:
1) Download and open attached project "TestLiquidOrgan.zip"
2) Make sure MSAA is on (2x seems to be enough)
3) Make sure HMD is connected and VR mode is on in Player Settings
4) Play scene and observe that the bottles are not transparent
5) Turn off MSAA and play again
6) Notice that the bottles are now transparent

Actual result: With MSAA and VR Mode the bottle transparency is not seen, it is black instead (see: https://gyazo.com/db903314f85a3d9aa9b40c28db08b312)
Expected: Bottles are transperant, regardless of MSAA or VR settings (see: https://gyazo.com/4c07e9b524c679cc4fe58334adb83ea2)

Tested and reproduce on:
Windows 10
Oculus CV1
Unity 5.6.0p3, 2017.1.0b3

Not reproducible in:
Unity 5.5.3p2

Verified FIXED 2017.2.0a1 and 5.6.2p1