You may want to consider Lyme disease as a possibility. Lyme disease is a multi-system bacterial infection caused from the bite of an infected tick. It often starts out as flu-like symptoms. Ticks can also transmit several co-infections, including ones that can cause a high fever.
When Lyme disease is a possibility, it is very important to see a knowledgeable doctor. No test is completely reliable. A negative test does not rule out Lyme. The best Lyme pediatrician is Dr. Charles Ray Jones in New Haven, CT. He sees patients from all over and has helped a lot of children. You may want to call his office for advice.
For more information on Lyme disease (including a symptom list), see the Lyme disease board at this site.
Keep searching, you will find out what is wrong. I hope your niece feels better soon.