Jan,
I just created a simple VI that inputs from a string control the string "0.000000001" and outputs, to a DBL, with the format/precision set to 10 digits of precision, and engineering notation, the value "1.0000000000E-9" (as a number of course.) The only input to the Fract/Exp String to Number function was the string. So, as long as you have those characters written in the file properly, and you have your indicator setup right, you shouldn't need to input anything else into the primitive.
Good luck.
If you need, I can submit the VI.