go into your profile and put your location. you'll get better location specific answers
i use screened bottom boards, but i put the insert in for about 8 or 9 months of the year. i find them convenient for swarm catching and mite checking, but don't want them open in winter.
it is normal for the bees to be near the top at this time of the year. they move up into the food over winter and move down in spring and summer.
how much was stored in each box? how full of bees were they? might you have left them to much space or not enough food? what do the empty hives look like? dead bees, dead on the bottom, stuck in the cells, in a clump, etc.?