The two answers already given deal with the situation from the in-universe point of view. I would like to point out an another approach to this problem. That is - the perception of intelligence (since OP used this term).
You seem to think that the usage of advanced tools is a definite proof of intelligence. For humans it is logical to view the world that way - we are definitely intelligent, and we are the only species to use spaceships and nukes, so one fact is connected to the other, right?
Wrong. Right? Maybe??? The fact is, humanity has no frame of reference on this matter. We do not know any other intelligent species that uses tools as advanced as ours. We are defined by our tool use, and our civilisation is inseparable from tools. But the only (possibly) intelligent species known to us (cetaceans and higher primates) use nothing like these. On the other hand, many animal species generally considered non-intelligent (to give some example, crows, beavers, coral polyps and banded acaras) do use primitive tools and/or construct quite intricate structures, but we do not take those as a proof of their intelligence. 693
We assume that dolphins and higher primates are intelligent based on other factors - that they apparently self-aware, that they have a language and seem to be able learn (to an extent) human and artificial languages, etc. And if the Bugger civilisation is as defined by their philotic communication as we are by our tool use - it would seem logical that they dismiss humanity as a species that although using intricate tools, seems to lack any (known to them) means of communication. Is it possible for a specie to evolve into using spacecraft and nuclear fission? Current data shows that it is highly unlikely... in Earth-like environment. In other enviroments - who knows? It is not proven to be impossible.
Thus, while it is possible that Bugger queens lied about knowing that humans are intelligent (either as individuals or as a hivemind) during the second invasion, that lie is at least believable. Just because you met a being that defends its territory and is efficient in that, does not mean it is intelligent. It just means that it is better adapted to its environment. And while "intelligence" currently seems as the best choice in adapting to Earth's environment, that might not be true in another environment.
P.S. I'm thinking that "sentience" would be a better term than "intelligence" in this question, but I am not a native English speaker, so I might be wrong. 350