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Whats the average temp you have them at? My guess would be bacterial infection if its not the temperature being too low.

I honestly couldn't tell you. Moving them would be the first step if possible, but for it to be on all of your queens it could be something about your room or wherever you are keeping them and thats assuming it is bacterial. I suppose I would try just absolutely sterilizing an entire tube setups worth of stuff. You could try immersion in rubbing alcohol for a while which would probably kill off anything. I would then move just one queen and only the queen, no brood, and place her in the new tube. Feed her but use new food that is from a different source than anything you are using now so she has enough energy to raise new eggs. Also try using distilled water.

But really I couldn't tell you. Might also be some sort of mites on them so place newspaper down where ever you put the new setup cause I've heard that it is might resistant and I haven't had problem so far with is when I was raising fruit flies.

Really everything is conjecture so definitely search into other options.

You both use plastic tubes, the obvious next step would be to switch to glass to see if the plastic tubes are somehow toxic When I did a larger project with this species to measure founding times with different numbers of queens:

http://antfarm.yuku.com/topic/1201

http://krungkuene.org/imgant/pic/100_2863.jpg

The majority of my colonies and queens were successful in founding colonies with very few brood casualties. I used all glass test tubes.