Yup If you are wondering, You make your stone tools with Smelted cobblestone (Which named "Stone"). I was having the same issue, I used to play hexxit and you do stone tools with cobblestone. But AOTBT has diffrent config file for that I guess... Like Big Dig, which you don't need any smeltery for making iron,steel and metal tinker tools.
In nutshell, Use Stone instead of Cobblestone in Tinkers Construct. Same for the repairing too.