Then, agents gave Dr. Tsonas a copy of his own notes from the emergency room visit and he read them. "I said, `Oh, my God, my written description is consistent with cutaneous anthrax,' " Dr. Tsonas recalled. "I was surprised."
The FBI was apparently on top of this before this doctor even remembered it -- it doesn't seem that they could find any trace of anthrax in places where the hijackers had been, which perhaps indicates that there had to be a separate facility involved. What if these guys had anthrax that was totally unrelated to the letters? What if there were multiple agents with anthrax? That might explain the inability to connect the dots between New Jersey and Florida.
My thoughts: It doesn't surprise me that no traces of anthrax were found in their apartments or vehicles. The anthrax was hermitically sealed (likely) and probably stored in a 'safe place', possible a medical clinic or doctor's office where they could divide and distribute it in friendly territory.
Also, these terrorists would likely have been innoculated with anthrax shots or have been provided medicine (Cipro?) as a preventative precaution. Such measures would have protected them to a degree, but not completely. These are my speculative thoughts, for what they're worth.