Duplicating Problem

hi guys, i duplicated a building and some of the bases didnt match, they were just more elevated than the original.


http://postimg.org/image/epki7yold/

now my guess is, it has something to do with how I built it, using sized pillars that didnt necessarily fit the gaps, but it ended up looking right on the original. when dupliacted it refitted the pillars so that the the ends matched up, casuing the ground elevation. Is this something that can be fixed, or do I need to be more careful with building originals?
 
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