The config servers don't do replication in the way that replica sets
do so you need to make sure you setup things correctly.
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It is also possible the data you found was old (left over from a
migration which failed); in scenarios like that you can duplicate or
data on the old shard. If you have deleted the data since then it will
look like the data is in the wrong place, but isn't really.
Is it possible that you wrote directly to the shard, not going through
mongos? This can also cause data to be on the incorrect shard, for
example.
From my experiences the most likely cause of problems like this is the
last option, writing directly to the shard.
http://docs.mongodb.org/manual/reference/config-database/
This page has explanations of all collections in the config db. All three config servers must have the same contents.
Asya
P.s. it's best not to add to a very old thread - start a new thread with your question.