“The frame you are speaking of is likely to be the frame that contained the eps logo in InDesign.” YES, it has nothing to do with the eps, it is used multiple times without this same effect.
“Has your printer offered an explanation as to how this may have happened, and if so, what was the explanation?” Printer: The file is bad, too many layers and colour modes. On investigation this is not the case.
“Does the printer have a procedure in place for handling non-conformance issues like this?” Apparently not. I am trying to resolve what the technical issue is. This will ascertain responsibility.
“Was this the only page that this happened on or was this throughout the document?” This happened throughout. 2 instances with the logo where the frame was assigned a background colour. Other areas where a frame has been added over a photo to fade to black background. This frame extended further than the photo in places. In the inDesign file, the same formula black was used on these overlays.
At this point, I am pretty sure that the rich black was altered at some stage, not taking in account these unusual instances and the result was these patches. I think inDesign is innocent. The original iD file is not perfectly constructed – in my opinion – with multiple people working on it, but colour-wise it seems correct.
There seems to be no technical reason or instance where rich black over an identical rich black should render this way.