I remember reading (I think on here) that farmers out in SD would use straight brassica cover crops but would end up with little to no residue.  If I recall the brassica's tipped the C:N scale and increased the soil biota so much that it ate up the residue too quickly.  So, they don't do straight brassica covers anymore.  It sounds like you are saying that the cover crop plots may have less residue than no cover, right?  That could explain some of it.