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FBI has always been pretty efficient in handling immigration checks.
I think they just run fingerprints through their database and send an OK to INS if no hits come up.
The real worry is the CIA checks. Those usually take pretty long and will take longer still now. Moreover, I heard that till recently INS had a policy of adjudicating I-485 petitions even if CIA clearance is still pending (The idea was that if CIA report indicates a problem, GC would be revoked).
Now this is definitely going to change.