Certain objects invisible when viewed through water

What I expected to happen was...:
Everything in the game looks as it does normally when viewed through water

What actually happened was...:
The inside of nether portals is invisible only showing the purple particles when viewed through falling water. Also, when underwater, clouds appear darker than the sky and clouds' sides are invisible

Steps to Reproduce:
1. Create a small screen of falling water with a view of the sky
2. Create a nether portal on either side of your water
3. View the nether portal from the other side of the water
4. Step in the water and view the clouds with graphics on fancy