Greetings, I've read that KIS might have some compatibility issues with TweakScale, but this maybe helps to resolve it someday (probably not ).
Tested with only KIS 1.2.12, TweakSkale 2.2.13 and ModuleManager installed. KSP 1.1.3 Steam.
Basically, if I put a part directly from the part list in to an inventory, it will have a cost of 0. Placing it on the craft first and then in the inventory resolves it. This happens only to parts, which can be resized with TweakScale, other parts will allways have the correct cost.
placed directly:
from craft: