I have a similar problem. With 5 shards, querying 500K rows fails, but 400K is 
fine.
Querying individual shards for 1.5 million rows works.
All solr instances are v4.2.1 and running on separate Ubuntu VMs.
It is not random, can be always reproduced by adding &rows=500000 to a query 
where numFound is > 500K

Is this a configuration issue, where some setting can be increased?

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