I can only guess were I do not have experience with what I have seen but here are my thoughts.

<I would expect to see some chemical response to queenlessness. Workers are programmed to lay in the prolonged
absence of queen pheremones, rather than simply abandon the hive.>

Could it have been so late in the season that a worker did not start to lay because the queen had stopped laying by then also?  This is Maine after all it gets cold by the end of October. There was capped brood but not loads, maybe three frames in the weaker hive they may not have had enough winter bees to survive. My note book is at the apiary, I am at home so I am guessing on how many frames of brood they had.

<I understood there was brood & stores in the abandoned hive. If so, I would be inclined to test pollen stores as well.>

Yes one hive did have pollen and honey, the other hive just pollen (I expected them to run out of food that is way I was keeping an eye on them and ready to try candy boards) when I found them empty. Both hives had brood, pollen, and honey at the end of October. But one was combination of two weak hives the other a swarm from June that I believe was never re-queened by the bees or me (did not see any queen cells on the frames when inspected this week). After thought always teaches one allot, next time I will consider re-queening swarms. I know most just shake the weak hives but I thought it wouldn't hurt to try and I may learn something. 
If the pollen is contaminated every hive in this yard will mostly will have the same problems but so far it has only been the weaker hives. There are 15 or other hives. It is a rural area with a few farmers market type farms around allot of woods and wild flower fields. One golf course who knows what they are doing but they have been there over twenty years with no problem and bee hives have been in this location for over 70 years.

This years was one of the worse springs and summers in the history of weather keeping records. It made a really good year for learning since the bees threw so many challenges and unusual things at me. My mentor has been a beekeeper and farmer for 78 years and he had never seen a year such as this. So a good year to gain knowledge a bad year for the bees. If every thing was picture prefect this year I guess I would not have had to think to hard. I'd rather deal with these things when I can have another set of hands and eyes to help, my mentor is 90 so my time with him is greatly appreciated because 90 is OLD. 

Karen

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