http://docs.mongodb.org/manual/core/replica-set-sync/#replication states:
For a member to sync from another, the buildIndexes setting for both members must have the same value/ buildIndexes must be either true or false for both members.

Not sure what the original intent of this statement was here, but this seems incorrect. If this were true you would never be able to initialize a buildIndexes=false secondary member from a primary.