Why are we getting different results from search heads in our Splunk 6.2.3 search head and multisite indexer clustering environment? Is this a replication issue?

Hi, We have an implementation of 3 search heads in a search head cluster and 4 indexers in a multisite indexer cluster all in Splunk 6.2.3. The search heads have search affinity (sh1 and sh2 site1 and sh3 site2). We have detected that doing the same search across the search head, we have different results. It looks like there is a problem with the replication across the sites. Checking the DMC all the index looks ok. Why this problem is not shown in the DMC? Is there a way to rebuild the index to the site that has the replication problem? Thanks,