No, it doesn't make any difference on your return. 

There are several reasons the program does not always "save" your answers. 

Many of the questions are only asked so the program knows what the next question should be. You may have already changed your answer, and need to change the follow-up answers. Finally, there are some questions the IRS wants to make sure you answer right before filing - for that reason they will have you confirm that answer on a final review.