When looking through block mixer blocks (BMB) made with non-opaque blocks (i.e transparent blocks), other BMBs don't render, you can see through them to the next "normal" block.
Example:
P -> T -> O -> N
P = player
-> = line of sight
T = transparent BMB
O = opaque BMB
N = normal block
In this example the player would see through the transparent BMB (good), and through the opaque BMB (bug) to see the normal block.

Also, you can see Project Red's illumar lamps through opaque BMBs, not sure if that is on you or them.

I should add, the transparency issue still occurs if you are looking through a transparent custom door frame. The issue occurs both if you use glass or if you use a custom liquid as the transparent part in the BMB.

Edit: The bug occurs only when the transparent BMB is touching another BMB (i.e. right next to one another), but it effects BMBs multiple blocks away when looking through a custom door (but only if the custom door has the water/ender effect, glass doesn't cause any issue).

Edit2: Not sure if this helps, because I don't know as much about texture rendering as I should, but here is a find. When looking through a door with the ender portal middle and looking at chisel's lavastone (the texture of flowing lava in the background and bricks in the foreground), all you see is the flowing lava. Perhaps it strips away the overlay on the custom texture, and that is causing the error? When looking at a carpenters block with a texture over it through an ender door, it looks normal, so maybe I am mistaken.

Edit3: Pictures for clarification (soulsand on bottom is a BMB): http://imgur.com/x4TwyWq http://imgur.com/abFoSDj http://imgur.com/vd2pikw

The pictures actually show 2 different things.

First, the face of fully opaque Mixed Blocks should be visible if next to a non fully opaque Mixed Block, or glass. That will be fixed in the next release.

Second, there is a Minecraft limitation with tansluscent TileEntities. TileEntity visible behind a another transluscent TileEntity is dependent on order of drawing and that's totally out of my control, So that part can't be fixed.

Anyway, thanks for the feedback.