@ismarc , I have never had to encounter your particular use case. Is there a bug report with details for duplicating this ? Like I said, I am not a fan of Mongo and were I to encounter an issue like yours in my use cases, I would bite the bullet and migrate to something else.
There may still be. The first two I opened were closed pointing to docs on how to set the writing stuff. The reproduction is pretty easy, if a shard tries to write its results to a shard that is write locked, none of that shard's map reduced data after that point is written to any shard. The more evenly distributed your data, and the more shards you have, the more likely you'll hit the condition. Combined with the fact that all unsharded collections always go to the same shard, the whole system becomes useless unless you can fit your entire dataset in all collections in ram on a single box.