Manuel,
The problem may not actually be Capture One's fault per se, but rather an issue with the encrypted (or "encoded") white balance. If Capture One is using Nikon's supposed mini-SDK for reading this encrypted white balance, then this could be the cause of the color shift. There are ways to work around using this mini-SDK with PM-captioned files that I devised for Thomas Knoll, and it sounds like Capture One will have to take a similar path. The issue of a resolution of 1 DPI is potentially a separate issue from the encrypted white balance, and could indeed be a failure of Capture One to properly parse the NEF file. PM can fix this resolution without having to open your file in Photoshop. See the Tools menu...
As far as a workaround, if you must use Capture One, then you could just use XMP sidecar files, then merge the XMP into a processed JPEG from Capture One (if that is your output) as long as the base filename is the same. Not ideal of course. What would be ideal is if everyone were to parse TIFF-based RAW files correctly.
--dennis