Try re-downloading the exe if taht doesn't work find your tekkit folder C:\Users\YOUR USERNAME\AppData\Roaming\.techniclauncher\tekkit backup your worlds and make sure you know any server ip's you want to keep delete tekkit folder and then reopen the exe then wait for it to download again.
Mine has done this too including texturepacks, I don't belive it is a misstake i think they are trying to store all of that information in 1 place deliberatly, just to make it easier for simple people to add texturepacks or edit configs that they cannot find in the .tekkit directory.