Why would recommender not submit letter to some schools?
You're right that there isn't any particular reason for a professor to intentionally and voluntarily refuse to send letters to certain institutions, especially not without telling you.

So I would consider unintentional and involuntary explanations.


The notification emails may not be reaching her (IT failures, spam filters, etc).  Try to contact her personally (email, phone, in person) and let her know that the letters are due.
Oversight is a possibility.  She might have forgotten about the letters and then gone on vacation where she doesn't see the emails.
She may be unable to work because of some sort of emergency (personal, family, medical, etc). Recommenders are people too, and sometimes things happen in their lives that take priority over your letter.  If you cannot contact her yourself, contact her institution or department and explain the situation.  It is possible that they will have access to a letter she's already written and can send it out, or that someone else there can write a letter.