Doctors knew the donor had encephalitis, an inflammation of the brain, when they harvested the organs. However, they didn't know rabies was the cause.
In this most recent case, the donor was experiencing "changes in mental status" before he died, according to Dr. Matthew Kuehnert, director of the CDC's Office of Blood, Organ, and Other Tissue Safety. He said doctors in Florida tested the donor for various causes of encephalitis, including West Nile Virus and herpes, but did not test for rabies.
Hospitals do test for other causes of encephalitis, and if no cause is found, the organs are donated.
The part that is most concerning is that the doctors knew the patient had encephalitis (granted not all causes of encephalitis are infectious in nature) and decided to donate the organs anyway.