Stone can be used to craft any stone variant both in hand and with the stonecutter. This is a survival world and the stone was created with a furnace (I don't have silk touch to try with those blocks.) 

I have been unable to reproduce the issue in new worlds or existing worlds. 

The only difference in their NBT data is that the bugged ones have the value 32767 in the Damage tag, whereas the normal behaving ones have a damage value of 0.