Not to repeat the obvious but;

(1) If they were hived late in the season, were the bees in "cluster mode", either then or shortly thereafter, i.e was the hive being actively ventilated and for how long?

(2) Were they hived in "flight mode" long enough to "varnish" the interior surfaces enough to to block "out-gassing" of formaldehyde, etc. ?  It is my understanding that Styrofoam never stops "evaporating" and "varnishing" is what would block the "out-gassing". 

I would surmise that this "seasonality" is the big issue with new Styrofoam hive parts.  FWISW, IMHO, the covers are the greatest but I'm here to doubt the rest of it is really worth the investment.

Rip 

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