OPINION-SPECULATION: I don't know what the search warrant contains, but this is interesting -- unknown if it is related to the search warrant.
http://news.google.com/news?hl=en&ned=us&ie=UTF-8&ncl=1114403087
They've recently purchased some aircraft from Boeing, too. Years ago there was a hijacking where the pilot was killed.' Their CEO keeled over in 05 or 06; not sure who runs it now.
There could be any number of things
My guess would be antitrust violations. Price fixing of certain routes, adding improper surcharges, something like that. British Airways, Virgin, American, are already under investigation.