In "Come, Let's Away", Braka is talking about the Federation in the present tense. I'm not saying the Federation ignored what was going on... I'm saying their arrogance and underestimating of Braka (and almost certainly of others we have not seen) led them to not consider him as large a threat as he should have been taken because they looked down at him. And historically, Starfleet and the Federation have been arrogant and condescending, so it is an established pattern of behavior.
Also, I can't believe it took Starfleet months to confirm omega was stolen... even worse is that confirmation seemed to happen ONLY because Braka used it in that empty sector. It definitely made Starfleet look either incompetent or were dragging their heels, and considering the base Braka broke into was such a classified high weapons place, it gives off more of an impression that they thought he couldn't use whatever he got so didn't bother to REALLY investigate hard and fast because they thought so little of him. Constantly underestimating an opponent is also a kind of arrogance.