Although examiners do the best they can, humans can make mistakes which the computer can catch. However, it is not a substitute for the manual examination, for although the computer can successfully catch missing and substituted letters, it can not determine letters with a problematic shape if they are Kosher or not, or do the actual repairs if necessary. This can only be accomplished through a meticulous manual examination by a qualified Sofer.
The cost for a computer examination is minimal and a one time expense. If you have never had your Teffilin or Mezuzos computer checked, it is advisable to do so the next time you have them examined.