According to one of the NYT reports:
<font face="Verdana, Arial, Helvetica, sans-serif" size="2">FBI spokesman Pete Gullota said an incident similar to the one Tuesday occurred shortly after the Sept. 11 terrorist attacks.
Gullota said an armed, off-duty FBI agent from the Baltimore office was not allowed to board a plane by a pilot despite following the security procedures for armed agents. Gullota refused to identify the airline but said the issue was cleared up and resulted in the pilot's suspension.</font>
I guess all's well that ends well.