Based on what, exactly ? Two 'sister-queens' (perhaps, but maybe not) - even if they did have the same mother, their fathers could have been different - so maybe one is producing a different 'mix' of pheromones than the other ?
The two colonies involved here have come from different sources - so why do you doubt that they express different behaviours ? Even if the queens involved are identical clones of each other, it takes time for the influence of new queens to produce an effect.
People sometimes talk almost as if a queen and a colony are discrete units which can be viewed as being independent from one another, and moved around indiscriminately like so many chess pieces - but they're not - there's also the neuro-biological relationship between queen and colony to take into account. A taste of this can sometimes be observed when introducing a queen into a colony with far different genetics. On one occasion I had extreme difficulty in getting a purchased queen to be accepted by a target colony, and so after a week of hostility I tried her with another colony from a different line - with almost instant acceptance. This sort of event is just a tiny window into a world which we barely understand the complexities of.
If the dynamics of initial acceptance can be so varied - then why not the ongoing effects of pheromonal differences too ? I'd say a colony is ultimately only as good as the relationship between it and the queen which 'heads' it, but also that each queen is only as good as the relationship between her and the colony within which she resides. When eventually she gets to head a colony exclusively of her own 'manufacture' (as it were), only then do we get to see a true picture of her biological potential. There are more variables involved here than anyone can shake a stick at, and the intervening period during which a queen temporarily heads a colony of another queen's bees only serves to add more.
LJ
