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You've got a good handle on why the FBI "mis anthraxed" this one. Basically, they get as good and capable agents as any other agency, even though they lowered their requirements. The requirements used to be a law or accounting degree, now any old degree and a Masters after joining (in what basket weaving?)- is my understanding.

Assuming that they have the agents they need, and the ones that were in counterintelligence, ie the Russian speaking ones were all pretty smart. Perhaps the Bureau moved the lesser mopes into the mainstream and promoted evenly from all areas thus putting more mopes into management. Perhaps this is wrong too, BUT, it is their management and entrenched culture whereby they believe their own press. As I recall they had two full time groups in NYC alone doing nothing but PR (easier than locating terrorists). Hope this factors into your thought patterns.

Works for me:

Various reasons for FBI, um, "disinformation," include:
- Smarts: the FBI, at the behest of the admin, is sowing disinfo while we prepare for checkmate.
("disinformation" is a comforting possibility, but highly unlikely at this late date)
- Liberalism: FBI management, promoted during the 90s, really believe the RW nut scenario.
(unfortunately, this is at least as likely as the "disinfo" campaign)
- Organizational vanity: The FBI, pop-psych profile in hand, is forcing the case to fit the profile.
(profiles have media glamour, but are easily subjected to political forces)
- Bureaucratic entropy: The FBI's mission and training focus is on domestic crime-fighting.
(when all you have is a hammer, every problem is a nail)
- Revisionism: FBI's focus on domestic extremists led to disasters at Ruby Ridge and Waco.
(therefore, a domestic, RW, anthrax nut would prove the FBI was "correct" all-along)
- Policy Problems: Faulty evidence rules and case policies from the 90's badly affect investigations.
(Rank-and-file grumblings: Trie; Wen-Ho Lee; Moussaoui; flight schools; OKC; etc.)
- Stoolie: The FBI is attempting to protect a mole or some other source of info.
(maybe they have someone on the inside, but it seems unlikely)
- CYA: They're covering for some yet-unknown, internal lapse or action.