Medical school admissions committee members are people. It would only be human for them to wonder why you didn't report the scores from your first attempt. Their attempt at pondering your motives should not be viewed as something that will get you rejected. If your GPA is good and the MCAT scores that you do report are good, then it is likely that you will be invited for an interview. At that time, it is possible that someone may ask you why you didn't report your first scores. At that time, you would explain to them your reason(s). Since admissions committee members are just people, it is safe to assume that they are willing to believe any legitimate excuse. Furthermore, you may not be the only one who is only reporting their second attempt. It's like they say, "there is safety in numbers."
So just to some up, it is true that they might wonder why you didn't report your first attempt, but it is unlikely that they will reject you only because of that reason.
Shelam
NYCOM, Class of 2002