Without being able to see the rash, I would be most concerned with a yeast/fungal rash, which could have been made worse while on the Augmentin. As you know, the Nystatin is an antifungal. If there is a persistent yeast/fungal infection despite Nystatin, then a trial of a different medicine, such as clotrimazole may be an option. It also may be an option to use an oral antifungal, such as fluconazole.
This may also be further complicated by the fact that her face and sinuses are not completely resolved, so she may need a longer course of antibiotics.
It is certainly possible that this could be a primary inflammation of the skin. There also can be involvement of the skin with lymphoma. However, the pattern of spreading from the vagina and the rectum is more often seen with a yeast/fungal infection.
Regardless of the cause, it also may be soothing to apply cool compresses or to apply topical lidocaine. Neither of these will treat the condition, but she may be able to be more comfortable.
If I can provide any additional information, please let me know.