What did you transcode the ProRes files into?
I ask this because I’ve noticed a similar (but not identical) issue. I’m working with ProRes MXF files (perhaps same as what you’re doing?), and my exports out of MC also exhibit a color shift.
Even a quicktime reference file (from ProRes MXF) will exhibit a change.
The only fix is to transcode my sequence into DNxHD, at which time there is no color shift on my exports. For now you may have to do the same.
My guess on what’s going on: The export dialog box gives you the option to output RGB (which takes the 16-235 values and pushes them out to the 0-255 range) or 709 (which leaves everything as is). I think exporting a quicktime from ProRes MXF is always forcing the 16-235 values to be shifted, even if you select the latter option not to do that.