This is something to do with Minecraft its self. its called Culling, it hides the faces that aren't seen in normal play, so if you use a full block like you are, it tries to hide faces of the blocks its touching because Minecraft thinks there is a full block there. To fix this just use blocks that ...

I have been running into this issue with every block texture I made for Minecraft.



I have no idea why but any block this textured block touches goes invisible.
I really appreciate any help as I cannot seem to find a solution to this so far.
Thanks in advance!