With my images which are always in RAW format .nef I cannot find a way that MC12 can interface and be able to capture any edits that I make using the Nikon Capture NX2 software. That is unless I make the edits then export to JPEG or TIFF and let MC manage the exported files. The problem with this is I have to manually manage 2 sets of files, which I am not going to do as I have close to 40,000 pictures. In addition there seems no way to synchronize the XMP/IPTC data managed in the Nikon SW with the metadata in MC, which is a further problem.
Welcome to the world of proprietary RAW formats and decoding. Pretty much no one except Nikon actually does things the 'Nikon' way. Lightroom (what I use for my photographs) completely ignores most of the proprietary Nikon stuff (like most in-camera color/curve/other settings) and uses it's own proprietary algorithms for decoding. As long as your are committed to using Nikon's software to manipulate your images, you are stuck in their sandbox until you export to TIFF or JPEG. Nikon does offer an API for getting at their data, but it is extremely limited. Any company that is serious about their RAW converter wants access to the actual sensor data, and the API doesn't give this information. To be fair, I have the same issue with Lightroom in that my edits are stored non-destructivly in side-car files or in the file itself (if converted to DNG) - but only Adobe's software that uses their Camera Raw engine can read and use those develop settings and edits.
I am pretty sure that JRiver still uses DCRaw to interpret the RAW data in to an image. Since DCRaw does not use the Nikon API, it will not 'see' most settings or changes you have done to those settings via Capture. Since it also does not use the Adobe Camera Raw (ACR) engine, it does not 'see' anything I have done to the image in Lightroom. It is just displaying the DCRaw decoded version of the original sensor data captured by the camera - before any exposure changes and adjustments.
For the record, this is not just a 'Nikon' issue.
JRiver has several choices when it comes to RAW files:
1) License and maintain the various API's from each camera vendor and incorporate the updates to their software as each one changes or releases new cameras. One major drawback here is that Canon has already 'obsoleted' some older RAW formats and removed them from their API. That means that using the current Canon API you would not be able to open/view images stored in a format used by some of their older cameras. Likewise, Nikon is releasing a new consumer P&S with 'RAW' capability - but it is using a new RAW format that is even unreadable by most of their own software at this time.
2) Create their own RAW engine (that would also ignore most of the 'in camera' stuff). This is not a trivial undertaking, would take time to get 'right', would require constant updating as new cameras and formats come out, and would be very expensive to do. It also wouldn't do a thing about your current problem with the RAW files edited in Nikon's software.
3) Use a third party RAW engine that already does everything they need for all cameras and is updated by that third party. Unless I am mistaken about DCRaw, this is what they have done.