Hi T.,
How are her other symptoms? If you put your ear to her chest, do hear pops, crackles, or wheezing? If so, please go back to see your doctor or the ER as this could be an indication of pneumonia which, BTW, could be either viral or bacterial. Although she might not have had a secondary infection the first two times you brought her in, it's possible one has developed since. More than likely, however, you're dealing with a long running virus and the fever should break soon.
These are the warning signs of something far more serious; if your daughter has two or more of these, high tail it back to the ER: rapid heartbeat (>90 beats/minute at rest), rapid respiration (> 20 breaths/minute at rest or panting), continued fever above 101.3 deg. F. Also, take her to the ER immediately if she has one of these symptoms: she is drinking fluids but cannot urinate for over 12 hours, or if she's refusing liquids and getting dehydrated, or if she complains of a severe headache, loses conciousness, or seems to be in an altered concious state. The above are signs of sepsis and/or meningitis/encephalitis and you do not want to delay treatment of these. Every hour of delay increases the risk of a mortality by almost 8%. Don't mean to scare you, but everyone should be aware of these symptoms for themselves and their children.
If the hospital you take her to has the ability to run a blood test for procalcitonin (PCT), you can try requesting the test. A PCT level greater than 0.1 ng/mL is a probable indicator of bacterial infection and antibiotics should be strongly considered. If the level is greater than 0.25 ng/mL, antibiotics are very highly recommended. If the doctor is unclear on these interpretations, direct him or her to the ProResp study: Stolz D, et al. Chest. 2007 Jan;131(1):9-19.
I hope your little one is back on her feet soon!