I wouldn't worry too much about the .040 but the .40 is alot unless its the rim itself and not an adjustment issue. 1/4" isn't a whole lot for the wheel to be out on the adjusters but the better you can dial it in the better off you are. When I true a wheel I try and get 0 movement from the dial indicator. Sometimes it isn't possible because its in the metal itself and not the spoke adjustment. If both measurements are .040 I wouldn't worry about it but if the .40 isn't a typo might want to have it trued.

I learned all I need to know about life by killing smart people and eating their brains.
Eat right ,Exercise ,Stay fit, Die Anyway!