When running a resource pack in chisel version 1.0.1.44 and CTM version 1.0.0.29, some connected textures of chisel blocks become nonfunctional. Issue demonstrated with pureBDcraft x64 here:

From top to bottom, circular bricks with CTM, sturdy factory blocks, lava brick (dent), and red antiblocks

I'm having the exact same problem on project ozone 3 using sphax 64x

The resource pack needs an update. See: Chisel-Team/ConnectedTexturesMod#111