Go to the opertors,  are they using gloves?  I found that in a no-clean processed assembly that had a really tight tolerance for contaminates because of the end use (military) that the assemblies would fail and when I watched the product being assembled the issues came from the operator's mainly in the through hole assembly process fingering up the components without gloves.  The board also collected contaminates from all of the operators who touched the boards but the majority was at through hole assembly.  

Kathy  

Kathy