What makes you think this is a civil privacy case? It is quite possible carrier iq was violating federal wiretapping statutes, which will put people into prison for years if convicted. In a criminal investigation you need to, you know, gather sufficient evidence and justification to get a search warrant so that you can dig into bits that are not out in public; a manual describing what the software actually does is one piece of data that would help in this case.
I don't buy it. I'm not aware of any similar investigation of a corporate entity like that, are you? What would be the point when you could just subpoena the relavant documents? Why must they have secrecy? I'm no law enforcement expert, but the kind of scenario you posit just doesn't seem to happen in the real world.
On the other hand, the FBI has been repeatedly caught with its hand in the surveilance cookie jar.
Seriously, given the available evidence you can't honestly say you find it more likely that the FBI is secretly investigating an existing company than that it's using that company's data for law enforcement surveilance. Can you?
* FBI Digital Forensics Agent: "Hey, did you guys see all of this data CarrierIQ is dumping to the phone unencrypted? Gold mine! Where is that manual?"
* FBI Wiretap Expert: "So these idiots are doing our work for us and sending it to people we already have a open subpeona with for cases X and Y. I wonder what else they are sending that the AD wants in those cases? Where is that manual?"
* FBI Field Agent: "The director just sent me this memo that Senator Franken included two queries about these CarrierIQ clowns in the last packet from the committee. Time to prioritize the investigation! We do have the manual and copies of that web site in our subpeona request file, right?"
All three are possible. All three could be happening concurrently. None of them are illegal and only one is ethically questionable. You have no idea what kind of scenarios happen in the real world, but in your world it seems that questionable surveillance is the only possible justification. I have provided alternatives and if I had to give an honest guess I would probably say that right now all three are ongoing, forensics probably noticed it first and told the wiretap guys while at this time the political/legal case probably has more agents working on it than the other two.