I grew up with Boxers and showed and bred a few litters and had several champions.
Anyhow, you may want to take her to the vet and get a skin scrapping done. She could have a type of mange or Seasonal Alapacia. (sp?) I've seen some bloodlines of Boxers with seasonal alapacia that would affect them with loosing hair in patches before, during or after their heat cycles. And those females would have it when they had a litter of puppies too.
If she had any type of mange you may be affected. So I doubt it's that.
It's just something to watch for.
The right dog food is very important too. As I've posted before, Grain free diets are the best (and only!) way to go.
A few things to think about when trying to figure out what she may have:
does she have deep wrinkles on her face? How are her eyes? Does she have smelly ears with any brown stuff or puss in them? Does she rub her face? Any excess tearing? Or dry eyes? Could she have injured her eye(s)? (My Boxers would play so hard or jump around and would scratch a cornea.) I would look at her teeth and gums too. Look for any type of abscess in her mouth.
Has she had her first heat yet? Or is she spayed? (I've seen spayed females have the seasonal alapacia too.)
She could be allergic to the shampoo that your using. A great shampoo to use (You should dilute any and all shampoos you use on her) is Micro tek. It's made by Equiss. It's great for any kind of skin problems.
I miss my Boxers! I'm waiting to find that right puppy to buy!
Good luck!