Simple guess: the NTF is spending time and efforts on something called ETAK. Don't you think it'd be logical to assume ETAK was something bad for the GTVA? If an outgunned, outnumbered and outclassed faction decides to focus on a project like ETAK instead of trying desperately to fill the gaps and match the GTVA, strategists should consider ETAK a powerful weapon.
This still does not explain why the GTVA didn't try to stop the Iceni. I don't view allowing the Iceni to slip by on numerous occassions as attempts on the part of the GTVA to stop the NTF from getting it. If ETAK was so dangerous, why the hell would the GTVA do exactly the opposite of what would stop it from being used?
That said, what happened in Deneb's asteroid field can be explained very easily. First of all, ETAK was thought to be a weapon of mass destruction supposedly uneffective against fighters and bombers. More importantly, at the time Alpha and Beta attacked the Boadicea, ETAK may have been unactive. Bosch was kind of afraid of that GTVA strike force, but that may have been bluffing. "I'm afraid, if you send your fleet I'll be doomed!" is the perfect way to actually lure the enemy and wipe it out.
Command may have anticipated Bosch's bluffing and reacted accordingly, ordering the blockade force to jump out. Evading direct contact with an enemy you know nothing about about is, most of the times, a wise move.
That's a lot of conjecture. For this to be true, you have to assume all of the following:
1) Command believed ETAK was a WMD
2) Command believed ETAK was ineffective against fighters and bombers
3) Command believed ETAK was capable of destroying fleets
4) Bosch was bluffing in an attempt to lure the GTVA out
5) Command knew this, and was also bluffing
Where did all these assumptions come from? This is an extremely contrived explanation for something relatively simple. Occam's Razor, I'm afraid. I'm sure you know the Latin.

Question: what's the point in letting the player scan the Iceni if SOC did it already? As far as I can say that was the first time an SOC unit faced the Iceni. Heh, the purpose of that whole operation was to learn more about the frigate. Why would SOC risk operatives to (re)gather info they already have?
The covert operation was to find more about ETAK. The GTVA probably knew about the purpose of ETAK, but not the specifics. They still wanted more data on ETAK. I didn't say the SOC already had scans of the Iceni, just that they already knew about the purpose and nature of ETAK.
Also, the objective of the mission was not to find more about the frigate. I don't even know where you got that from.
But you've said it there: if the GTVA had no idea what ETAK was then why did they fail to mount a serious capture operation when they had numerous chances?
Perhaps they wanted Bosch to complete his research before mounting a capture. Once Bosch's regime begins to collapse, they do attempt to capture - They succeeded in capturing the Sunder (which probably contained ETAK-related ****) and later the ETAK schematics ("Return to Babel").
I don't see that command 'allowed' anything. The GTVA quite obviously outmatched the rebels but that's not to say the NTF was not perfectly capable of protecting their assets, namely ETAK. It's possible that inbetween 'The Place of Chariots' and 'The Romans Blunder' that the deal Bosch was talking about (withdrawing his forces from Sirius) came to fruition and in return allied command removed the blockade. I was under the impression that the GTVA was occupying Sirius from then on until Koth struck back and wiped out the 6th Fleet.
It's heavily implied in Romans Blunder that Command allowed Bosch to escape. It's possible that the negotiation with Command did go through and Command allowed Bosch to escape in return for Bosch withdrawing from Deneb, but given the losses the NTF had apparently taken following the Aquitaine's entry (namely the loss of the NTD Jacobus referenced in Surrender Belisarius), the NTF was clearly on the backfoot and in retreat anyway. Additionally, the Psamtik was deployed to destroy the Impervious and Glorious regardless of any deal, which sounds a bit underhanded on Command's part.
Sirius did not fall to the GTVA until much later in the campaign. A two-pronged offensive on Sirius organized from Alpha Centauri and Deneb is described as failing (concurrent to Koth's offensive in Epsilon Pegasi). Sirius is described as falling after the Psamtik destroyed the NTD Cyrene (at the outset of the SOC loop).
Iceni escaped of it's own volition (no pun intended) in 'The Place of Chariots'. Delta wing was able to give it a good pounding yes, but they were unable to disable the ship.
This supports my theory that Command initially intended to destroy ETAK (and the Iceni, and Bosch) at that time but changed his mind between Place of Chariots and Romans Blunder.
Like I said it's possible that Bosch's deal regarding Sirius went ahead. Not to say allied command was not unaware of ETAK's nature though.
The deal with Bosch might have gone through, but considering how the NTF were already losing by that point, I don't see why Command would do this. As I said before, GTVA forces destroyed other ships withdrawing from Deneb at that point (a couple freighters, plus the Impervious and Glorious), if there was any deal Command probably went back on his word.
I'm fairly certain Admiral Petrarch speculated on ETAK being a WMD, but I could be wrong. It might have been he was attempting to hide the higher-ups knowledge of what they suspected the device really was or he really didn't know.
AFAIK the only references were from Loukakis and the SOC dude who explains your assignment undercover with the NTF. Petrarch did not speculate.
I suspect now though that contrary to what I stated earlier the Vasudan half of the GTVA genuinely hadn't any idea what ETAK was while the Terran half may have had some knowledge. Admiral Ahmose may have somehow stumbled across Terran-held information regarding the device and decided that the possible threat to the Vasudan species was too great to ignore. So he acted.
Vasudan elements were involved in the capture of the ETAK schematics (GVT Qeb, despite being a Terran Argo transport, was crewed by Vasudan marines). Either the Vasudans were being used as pawns or Vasudan Tactical Command had at least some knowledge of ETAK's purpose.
Exactly, 6 months! That's definitely enough time for the GTVI to have worked up some clue as to what ETAK was. Obviously not full knowledge or else Snipes wouldn't have been asking for a scan of the Iceni, but perhaps a small glimpse into the nature of the device.
Umm. My position is exactly that. The GTVA knew what ETAK was and wanted it.
Yeah cos we all know how wise command is.
Seriously though the GTVA isn't known for being cautious. Hell when the Shivans showed up they chased the bastards into the neula and beyond. Those are some real cojones right there!
Agreed. Note also the sacrifice of the Phoenecia against the Sathanas in eerily similar circumstances.