Responding to DYP...
Curious about the issue with color management changing when layout options (step-and-repeat, nesting) are selected. I just tested in version 6.4 with stunt profiles tagged to the images in a tiff and mixed RGB and CMYK content PDF with output intent. These profiles change color significantly to help detect if they are being used or ignored. From my testing ICC conversions are working as expected in both CPSI and APPE engines with both step-and-repeat and nesting. I do know that the CPSI engine is different in that it will not exclude embedded profiles – if they are there, they will be used, but that is written into the engine by Adobe.
Maybe it is something that changed from early versions of 6, or something was corrupt in the workflow/profiles/etc.
For the original post from Mark...
Color Profiler Suite is the same color engine that Fiery XF uses when Color Profiler option is enabled – it's designed for both applications. Later versions of CPS 4 stand-alone can connect directly to a Fiery XF server for profiling wide-format.