Default setting value for keeping virus defs on SEP 12.1 client would be = 1 revision.
What folders are all those duplicates contained in?
The is a known defect regarding amount of AV deinitions kept on SEP client in 12.1 - all versions of 12.1 below RU2 are affected:
http://www.symantec.com/business/support/index?page=content&id=TECH180056
..this is monstly seen on servers OS but you can go ahead and try the steps recommended here as well.