Hm, I seem to have a similar problem with one of my Water queens. (Sorry for hijacking the topic, but I think the problem's close enough to not warrant a new topic of its own.)
I was trying for Ocean bees, and ended up with a Water-Common hybrid queen who now refuses to work in her underwater hive. I've also got the "Hostile Environment" flag on the hive when she's in it. The hive is placed inside the first layer of water (so that it's in the water, but still gets daylight); there are Lily Pads around; and it has it's "back" to the bank, which is covered in flowers. Two blocks from it, same kind of position, there's another hive with simple Water bees who're working perfectly well. And until now, the problematic hive worked well too when it was used for Water bees only.
My Queen's traits are as follows:
Species: Water -- Lifespan: Shorter -- Speed: Slowest -- Pollin: Slowest -- Flowers: Lily Pad -- Fertily: 2x -- Area: 9x6x9 -- Effect: None -- Climate: Normal -- Temp. Tol: (0) -- Humidty: Damp -- Humid.Tol: (0)
Species: Common -- Lifespan: Shorter -- Speed: Slowest -- Pollin: Slowest -- Flowers: Flowers -- Fertily: 2x -- Area: 9x6x9 -- Effect: None -- Climate: Normal -- Temp. Tol: (0) -- Humidty: Normal -- Humid.Tol: (0)
In both cases: Nocturnal: No -- Flyer: No -- Cave: Yes
I tried to put her in a normal hive above ground, right next to the water, flowers and lily pads, just for testing purposes; but she still won't work. I'm still quite new myself to bees breeding, so I'm not sure what I should do now to make her work. Put her in the Acclimatizer, surely, but what kind of item should I use to acclimate her? (My aim is to get to Ocean Bees, then Stained, so evidently I want them to go on along the Aquatic Branch.)