Resource Packs cannot find specific textures "Missing"

Loading up a resource pack returns missing textures for many blocks... included is a list of the blocks affected and a screen shot;

Note: None of the textures are edited in the resource pack.

Affected Blocks:

• Stone
• Grass
  • Affects both side and top textures
• Cobblestone
• Bedrock
• Sand
• Gravel
• All Ore Blocks; (ex. Coal Ore)
• All Ore Storage Blocks (Ex. Coal Block)
  • Strangely Prismarine is unnafected
• Dry or Regular Sponge
  • wet works fine
    *Glass
• Dirt
  • Coarse Dirt is unchanged (looks fine)
  • Podzol also shows up normally
• Bookshelf
• Moss Stone
• Obsidian
• All Stair Blocks
• Both Ice Blocks (packed and normal)
• Snow
• Clay
• Pumpkin
• Netherrack, Soul Sand and Glowstone
• Jack O Lanterns
• Mycelium
• NetherBrick
• Endstone
• Hardended Clay's default state (dyed clays show up fine)
• All Leaf Blocks
• Crafting Table
• Furnace (Both States)
• A Lot More That I Cant list at the moment