Just a thought I assume that the queen you bought was marked and the frames you gave her in the nuc carried the main hive queen (you saw an unmarked queen) This would leave the main hive queenless so they start queen cells you leave some in the main hive and start another nuc 2-3 weeks later they are empty given this and the time line and the fact they are all in a weak state. Could they have swarmed( not sure of seasons in your area) and left, leaving the hives really short of bees which queenless followed the robbing bees back to their hive or possibly killed off by the robbers just as Finsky and apis629 surmises.
If the above is correct 1 unhappy mistake (the accidental transfer of queen) has lead to this, althought it would seem the splitting was possibly late in the year. Try it next time when there is a good flow early in the year and you will hopfully have a good outcome.
Diver