This behavior is actually normal. When you run a MathScript VI, the MathScript text code is compiled and converted to LabVIEW code, which is then saved in the form of a VI in the directory you mentioned. Doing this increases performance by giving LabVIEW a precompiled version of the MathScript code that can be used the next time it is executed. All of this is meant to go on behind the scenes, though, so it should be of no concern to the customer. If LabVIEW is compiling MathScript code for the first time, it will simply create a new VI, so there is no need to include these VIs when transporting source code.