I don't know if it's possible but I would try to isolate the bins where a rat dies and see if others start dying too. In a situation like this meticulous record keeping helps a lot. If it is genetic you'll be able to pinpoint who carries the bad genes and eliminate them from your breeding stock.
I would also makes sure they aren't overcrowded and that everyone has access to food. I just noticed for the fist time a rat being food aggressive to the point that the others around it were not eathing normally.
Rats are hardy animals so altitude isn't a factor I would consider but their is the potential for parasites. You could have a vet do a necroposy on t the next one that dies.
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