Hi Emanuele,
PixInsight respects the original FITS headers. Certainly, it also adds some private FITS header keywords, mainly to identify itself and to support some features (like ICC profiles for example), but if you open a FITS image and save it with PixInsight, no keywords are lost. Anyway, you can always save and restore the original FITS header of an image:
1. Open the FITS file.
2. Select File > FITS Header
3. Save a process icon from the FITSHeader tool.
4. Process your image.
5. Apply the FITSHeader process icon you saved in step 3
6. Save your image as a FITS file.
On the other hand, PixInsight fully supports 8, 16, 32 and 64-bit FITS images (64-bit integer images are not writeable), and it generates fully standards-compliant FITS files. You can check it with NASA's FITS verifier application:
http://fits.gsfc.nasa.gov/fits_verify.htmlSo I suspect the problem here is not in the FITS headers, but somewhere else.
As a footnote, I personally don't like and don't recommend the G2V color calibration method (or any other method based on particular spectral types), as I think it is neither necessary nor reliable, but that's another (long) story.