If you need a master flat that works with PI calibration then I think you'll need to build it in PI. The FITS standard doesn't specify the range of floating point values and I'm pretty sure that CCDStack and Nebulosity don't use the same 0..1 range as PI. Maybe you can fudge around this with the FITS format preferences and/or a bit of PixelMath but flats are very fickle! Another quick & dirty option would be to convert the master flat to 16-bit unsigned in CCDStack or Nebulosity before using it in PI. You'd lose precision but at least the range of values would match.
Cheers,
Rick.