I had same issue with cRIO 9064. Grate job solving and explaining this.
I have lost a day on debugging before I found what is going on.
Does this refers to all cRIOs or just 906x series? Document below refers only to cRIO 9063
https://knowledge.ni.com/KnowledgeArticleDetails?id=kA00Z000000kJlDSAU&l=pl-PL