Solr's deduplication via the SignatureUpdateProcessor is broken for distributed updates on SolrCloud.
Looking again at the SignatureUpdateProcessor code, I think that indeed this won't currently work with distrib updates. Could you file a JIRA issue for that? The problem is that we convert update commands into solr documents - and that can cause a loss of info if an update proc modifies the update command.
I think the reason that you see a multiple values error when you try the other order is because of the lack of a document clone (the other issue I mentioned a few emails back). Addressing that won't solve your issue though - we have to come up with a way to propagate the currently lost info on the update command.
Please see the ML thread for the full discussion: http://lucene.472066.n3.nabble.com/SolrCloud-deduplication-td3984657.html