"Nikon has very cleverly prohibited all other softwares like photoshop from opening their raw files" - This is not the case. Nikon has a proprietary raw format, as does Canon. If the camera you use was released onto the market at a date later than the version of Adobe Camera Raw you use, chances are you will need to upgrade ACR to be able to read the latest raw formats. As Ram points out, you will need Photoshop CS3 because the latest versions of ACR are not available for CS2.
I use Photoshop CS3 and Capture NX, I often run both at the same time and open the same images in both, I have no problems with different file formats and have uploaded images created by both Capture NX and Photoshop. This site being predominantly Canon I doubt everybody experiencing this problem on Treknature has installed Capture NX.
Logically the only way the format of a JPEG file could change through software such as Capture NX is to edit the image using that program and for that program to write the format differently. Capture NX or any other piece of software cannot influence the way Photoshop creates a JPEG format file.
I think some communication from the site admins on this would be useful now, there doesn't appear to be any progress with this problem.