since you are not mentioning any replication in your question, I would suggest to check
indexes.confon both servers if they are the same
outputs.confused by any sending forwarder if they are using both indexers or just one
forceTimebasedAutoLB = truein
Hope this helps to get you started ...
Is it the indexes that make the difference. Check your "Path to indexes" and is the size of the disk/folder of splunkdb on both indexers is the same? If yes, your indexes are being replicated properly but there is some other problem on one of your indexers.