I would imagine that you'd complain about something like a hernia. If you don't notice or report symptoms, what is she to look for? You are a fairly young man. I don't think she is shy or reluctant but in a physical, they expect you to bring up issues. If you don't, they do the basic check of that area. Do you suffer health anxiety?
Yes, it is unusual, but I believe that you have misunderstood her reluctance about fully examining you and interpreted it as "shyness". I tend to think she doesn't KNOW you well enough to believe that you will not scream "rape" if she examines as thoroughly as she should. I would urge you to ask her to include the genital exams when she does her physical work-ups. Tell her it will ease your concerns about your overall health if she does. She can request a nurse or an orderly to be present when she examines you.